| St Vincent de Paul Village Inc | 501(c)(3) | 1994 | $68.1 million | $70.5 million | 2024-12 |
| Forever Balboa Park | 501(c)(3) | 1999 | $6.8 million | $14.4 million | 2025-06 |
| Urban Street Angels Inc | 501(c)(3) | 2014 | $5.5 million | $1.5 million | 2024-12 |
| Catholic Community Foundation of San Diego | 501(c)(3) | 2016 | $5.1 million | $38.6 million | 2024-12 |
| Sola Media | 501(c)(3) | 2011 | $3.1 million | $2 million | 2025-06 |
| Jewish Community Camp and Retreat Center Inc | 501(c)(3) | 2002 | $2.9 million | $3.9 million | 2024-12 |
| Hindu Mandir Society of San Diego Inc | 501(c)(3) | 1995 | $2.3 million | $5 million | 2024-12 |
| International Bodhisattva Sangha | 501(c)(3) | 2006 | $2 million | $2.3 million | 2026-05 |
| M C Fathers Inc | 501(c)(3) | 1999 | $1.9 million | $232,921 | 2025-06 |
| Yad Ahava Foundation | 501(c)(3) | 2024 | $1.2 million | $10,065 | 2025-12 |
| Elisha Revolution Inc | 501(c)(3) | 2019 | $1.1 million | $96,230 | 2024-12 |
| Activated Ministries | 501(c)(3) | 1999 | $1 million | $1.9 million | 2024-12 |
| Redemption Evangelistic Ministries | 501(c)(3) | 1994 | $994,849 | $50,905 | 2025-12 |
| Coastal Christian Ministries Inc | 501(c)(3) | 2017 | $859,112 | $93,696 | 2024-12 |
| HR Ministry Solutions | 501(c)(3) | 2019 | $775,210 | $112,086 | 2025-12 |
| Beam Kenya | 501(c)(3) | 2016 | $728,623 | $744,115 | 2025-12 |
| Christ United Methodist Ministry Center | 501(c)(3) | 2014 | $626,932 | $954,771 | 2024-12 |
| C3 Church Americas Inc | 501(c)(3) | 2020 | $536,265 | $176,050 | 2017-12 |
| Thresholds Community | 501(c)(3) | 2013 | $444,299 | $276,770 | 2025-12 |
| Heritage Christian School of San Diego | 501(c)(3) | 1998 | $407,244 | $474,529 | 2025-07 |
| Sri Lakshmi Venkateswara Temple and Cultural Center | 501(c)(3) | 2021 | $397,795 | $824,128 | 2025-12 |
| Modern Catholic Pilgrim | 501(c)(3) | 2019 | $394,527 | $168,389 | 2023-12 |
| Jesus Is the Answer Inc | 501(c)(3) | 2008 | $371,517 | $8 million | 2024-12 |
| Kolping Youth International | 501(c)(3) | 2011 | $358,154 | $0 | 2024-12 |
| Butterfly Project | 501(c)(3) | 2016 | $345,751 | $229,984 | 2024-12 |
| Shiviti | 501(c)(3) | 2015 | $345,426 | $194,649 | 2024-12 |
| Catholic Action for Faith Andfamily | 501(c)(3) | 2007 | $342,444 | $182,699 | 2023-12 |
| One Message Foundation Corporation | 501(c)(3) | 2015 | $317,503 | $202,785 | 2025-12 |
| Submerge Church | 501(c)(3) | 2023 | $308,000 | $279,437 | 2025-12 |
| Muslim American Society of San Diego County | 501(c)(3) | 2013 | $295,870 | $1.3 million | 2023-12 |
| The Journey With Jesus Foundation | 501(c)(3) | 2005 | $293,827 | $70,273 | 2026-06 |
| Be2live | 501(c)(3) | 2010 | $291,496 | $42,148 | 2024-12 |
| Amigos 2 Familia Inc | 501(c)(3) | 2022 | $276,905 | $191,392 | 2025-12 |
| Palbar Ling Center Inc | 501(c)(3) | 2018 | $266,597 | $608,012 | 2025-12 |
| Mikael | 501(c)(3) | 2022 | $252,889 | $1.5 million | 2024-12 |
| Emerging Leadership Initiative | 501(c)(3) | 1998 | $223,668 | $305,378 | 2024-12 |
| Bridge Builders Network | 501(c)(3) | 2016 | $221,546 | $38,328 | 2025-12 |
| His Hands of Hope | 501(c)(3) | 2015 | $221,073 | $19,457 | 2025-04 |
| Wat Lao Boubpharam of San Diego | 501(c)(3) | 1999 | $201,553 | $1.9 million | 2023-12 |
| Global Ministry Resources | 501(c)(3) | 2016 | $199,000 | $1 | 2023-09 |
| Phat Da Buddhist Congregation Inc | 501(c)(3) | 2000 | $196,384 | $766,123 | 2025-12 |
| Jteen of San Diego- Soul X | 501(c)(3) | 2015 | $184,703 | $80,828 | 2025-12 |
| Iglesia de Cristo Armonia Ministerio Llamada Final Inc | 501(c)(3) | 2013 | $174,288 | $4,067 | 2024-12 |
| San Diego Shirdi Saibaba Spiritual Center | 501(c)(3) | 2011 | $169,201 | $550,055 | 2025-12 |
| Macintosh Ministries Inc | 501(c)(3) | 2018 | $159,604 | $105,858 | 2025-12 |
| Flood Church Association | 501(c)(3) | 2015 | $158,147 | $1 | 2026-08 |
| Conexa Inc | 501(c)(3) | 2016 | $149,239 | $82,007 | 2024-12 |
| Children Ministries International | 501(c)(3) | 2013 | $142,174 | $65,399 | 2025-12 |
| Beth El Endowment Foundation | 501(c)(3) | 2001 | $131,981 | $3.2 million | 2025-06 |
| Diadem Advent Hope Ministries International | 501(c)(3) | 2021 | $126,435 | $23,046 | 2025-12 |
| SD Crescentwood Services | 501(c)(3) | 2023 | $116,919 | $286,325 | 2025-12 |
| Joyous Community Church | 501(c)(3) | 2023 | $116,726 | $23,737 | 2024-12 |
| New Bethel Baptist Church of San Diego | 501(c)(3) | 1995 | $115,253 | $269,449 | 2025-12 |
| Reaching the Unreached Inc | 501(c)(3) | 2008 | $115,064 | $2,484 | 2025-12 |
| Samaria & Beyond Ministries Inc | 501(c)(3) | 1997 | $110,407 | $366,917 | 2025-12 |
| Renewal | 501(c)(3) | 2015 | $109,722 | $16,222 | 2025-12 |
| Rosaorito Beach Christianfellowship | 501(c)(3) | 2006 | $99,076 | $139,291 | 2024-12 |
| Prabhupada-Gurudeva Hare Krsna & Vedic Culture Museum Foundation | 501(c)(3) | 2019 | $98,416 | $195,100 | 2025-12 |
| Iglesia de Cristo San Diego Inc | 501(c)(3) | 2004 | $95,231 | $35,330 | 2020-12 |
| San Diego Community Kollel | 501(c)(3) | 2023 | $85,519 | $80,695 | 2025-12 |
| Compassion for African Villages | 501(c)(3) | 2007 | $81,475 | $83,073 | 2025-12 |
| Comunidad Siervos de Cristo Vivo | 501(c)(3) | 2004 | $79,091 | $0 | 2024-12 |
| 3XL Inc | 501(c)(3) | 2014 | $71,995 | $103,262 | 2025-12 |
| Divine Mercy Movement of San Diego | 501(c)(3) | 2023 | $70,805 | $52,677 | 2025-12 |
| Jubilee Economics Ministries | 501(c)(3) | 1999 | $70,502 | $12,708 | 2025-12 |
| Touch Life Mission | 501(c)(3) | 2008 | $69,796 | $1.5 million | 2025-12 |
| Coram Deo Ministries of the Christian and Missionary Alliance | 501(c)(3) | 2024 | $69,673 | $17,691 | 2025-12 |
| Faithroots Inc | 501(c)(3) | 2025 | $67,988 | $62,100 | 2025-12 |
| Upper Room Ministry of San Diego | 501(c)(3) | 2022 | $67,900 | $94,221 | 2025-12 |
| Iglesia Vision Apostolica Inc | 501(c)(3) | 2024 | $66,802 | $25,682 | 2025-12 |
| Heart of Mindfulness | 501(c)(3) | 2024 | $63,312 | $33 | 2025-12 |
| Soulwakening Inc | 501(c)(3) | 2023 | $60,472 | $14,350 | 2023-12 |
| Tabernaculo de Avivamiento Cristo Rey Inc | 501(c)(3) | 2005 | $60,238 | $3,938 | 2025-12 |
| Africa New Hope Empowerment Inc | 501(c)(3) | 2023 | $58,381 | $30,550 | 2025-12 |
| Experiencing God Christianfellowship Inc | 501(c)(3) | 2006 | $55,235 | $1 | 2024-12 |
| Gateway To China Ministries Inc | 501(c)(3) | 2009 | $53,282 | $42,592 | 2024-12 |
| Hoi Tong Do Toma Thien-Thomas Thien Apostolic Association | 501(c)(3) | 2000 | $48,550 | $31,608 | 2025-12 |
| Vietnam Great Tripitaka Foundation | 501(c)(3) | 2022 | $44,656 | $93,211 | 2025-12 |
| Sovann Kiry Cambodian Buddhist Society Inc | 501(c)(3) | 2012 | $44,094 | $756,318 | 2019-12 |
| Shoulder To Shoulder Ministry International | 501(c)(3) | 2010 | $33,876 | $17,228 | 2025-12 |
| Indo-Chinese Association of San Diego Inc | 501(c)(3) | 1995 | $30,000 | $913,726 | 2026-05 |
| Theravada Buddhist Association of Ca | 501(c)(3) | 2018 | $27,800 | $22,145 | 2019-12 |
| Quan Am Monastery Inc | 501(c)(3) | 2015 | $27,584 | $27,150 | 2025-12 |
| Quan the Am Thien Vien | 501(c)(3) | 2000 | $25,271 | $1.4 million | 2025-12 |
| Betty Upham Gouraud Music Foundation for All Souls Church | 501(c)(3) | 2010 | $19,705 | $438,968 | 2024-12 |
| Desention House Ministries | 501(c)(3) | 2020 | $14,420 | $148,593 | 2024-12 |
| The Van Phuoc Buddhist Center | 501(c)(3) | 2008 | $12,212 | $266,032 | 2024-12 |
| JC Stewards Inc | 501(c)(3) | 2015 | $9,519 | $267,984 | 2024-12 |
| Life & Strength | 501(c)(3) | 2014 | $6,369 | $2,837 | 2025-12 |
| Beachhead Ministries | 501(c)(3) | 2015 | $3,932 | $1 | 2024-12 |
| 2 Feet 1 Goal | 501(c)(3) | 2017 | $0 | $0 | 2024-12 |
| 242 Church San Diego | 501(c)(3) | 2012 | | | |
| Abbas Faith Mission | 501(c)(3) | 2004 | | | |
| Abundant Community Enrichment Programs Ministry | 501(c)(3) | 2023 | $0 | $0 | 2025-12 |
| Abundant Grace Christian Center | 501(c)(3) | 1998 | | | |
| Acts2 Southern California | 501(c)(3) | 2022 | | | |
| Adams Avenue Crossing | 501(c)(3) | 2009 | | | |
| Addis Kidan Ethiopian Evangelical Church | 501(c)(3) | 2012 | | | |
| Agape Myanmar Mission | 501(c)(3) | 2015 | | | |
| Aim San Diego-West | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| Aleph Baja | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Alkalam Institute Inc | 501(c)(3) | 2023 | $0 | $0 | 2025-12 |
| All Nations Fellowship | 501(c)(3) | 2019 | | | |
| All Peoples Church | 501(c)(3) | 2008 | | | 2013-12 |
| Amen Mission | 501(c)(3) | 2001 | | | |
| American Indian Ministries | 501(c)(3) | 2023 | $0 | $0 | 2025-12 |
| Amicus Presbyterian Church | 501(c)(3) | 2019 | | | |
| Amistad Cristiana Internacional | 501(c)(3) | 2003 | | | |
| Ancho Foundation Inc | 501(c)(3) | 2026 | | $20,100 | 2025-12 |
| Anchor & Hope Church | 501(c)(3) | 2024 | | | |
| Anchor Baptist Church of San Diego | 501(c)(3) | 2024 | | | |
| Ang Mga Kaanib Sa Iglesia NG Dios Kay Kristo Hesus Haligi at Saligan | 501(c)(3) | 2001 | | | |
| Antivenom Recovery Ministry | 501(c)(3) | 2022 | $0 | $0 | 2025-12 |
| Apostles of the Holy Spirit Inc USA | 501(c)(3) | 1998 | $0 | $0 | 2025-12 |
| Apostolic Ministries Prince of Peace | 501(c)(3) | 2014 | | | |
| Apostolic Monastics Inc | 501(c)(3) | 1998 | | | |
| Arete Theological Ministries | 501(c)(3) | 2016 | $0 | $0 | 2025-12 |
| Aroma Foundation | 501(c)(3) | 2023 | | $8.5 million | 2024-12 |
| Arsha Drishti | 501(c)(3) | 2019 | | | |
| Arsha Prasada | 501(c)(3) | 2026 | | | |
| Ascension Catholic Parish in San Diego Ca Real Prop Support Corp | 501(c)(3) | 2019 | | | |
| Assemblies of God International Fellowship | 501(c)(3) | 2006 | | | |
| Association for Integral Spirituality Inc | 501(c)(3) | 2002 | | | |
| Association of Christian Fellowships Inc | 501(c)(3) | 2004 | | | |
| Awaken Church | 501(c)(3) | 2007 | | | 2020-12 |
| Bais Betzalel Chabad of Rancho Bernardo-Poway | 501(c)(3) | 2025 | | | |
| Baptist Ministers Fellowship of San Diego | 501(c)(3) | 2011 | $0 | $0 | 2025-12 |
| Beloved Christian Church Disciples of Christ | 501(c)(3) | 2019 | | | |
| Berean Christian Fellowship Inc | 501(c)(3) | 2020 | | | |
| Beth Jacob Educational Center | 501(c)(3) | 1998 | | | |
| Bethany Community Church San Diego Incorporated | 501(c)(3) | 2001 | | | |
| Bethesda Tabernacle | 501(c)(3) | 2002 | | | |
| Bethlehem the House of Bread | 501(c)(3) | 2006 | | | |
| Blair Holloway Ministries Inc | 501(c)(3) | 2007 | $0 | $0 | 2025-12 |
| Blessed Assurance Baptist Church | 501(c)(3) | 2006 | | | |
| Blessed Sacrament Parish in San Diego-Ca Real Property Support Cor | 501(c)(3) | 2019 | | | |
| Body of Christ Community Church | 501(c)(3) | 2004 | | | |
| Bramblebush Inc | 501(c)(3) | 2005 | $0 | $0 | 2025-12 |
| Bread of Life Bible Fellowship | 501(c)(3) | 2004 | $0 | $0 | 2025-12 |
| Bread of Life Christian Church in San Diego | 501(c)(3) | 1999 | | | 2025-12 |
| Bridge Mission | 501(c)(3) | 2016 | $0 | $0 | 2025-12 |
| Brighter Day Ministries Church of God in Christ | 501(c)(3) | 2002 | | | |
| Brilliance Church | 501(c)(3) | 2026 | | | |
| Brothers of the Little Oratory in San Diego | 501(c)(3) | 2008 | $0 | $0 | 2023-12 |
| Buddhist Meditation Center of San Diego | 501(c)(3) | 2006 | | | |
| CFSSD Inc | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| California New Church Board Inc | 501(c)(3) | 2008 | | | |
| California School of Evangelism Inc | 501(c)(3) | 2021 | $0 | $0 | 2023-07 |
| Calvary Baptist Church | 501(c)(3) | 2014 | | | 2019-12 |
| Canyon Ridge Baptist Church | 501(c)(3) | 2019 | | | |
| Carmel Church | 501(c)(3) | 1999 | | | |
| Carmel Mountain Church | 501(c)(3) | 2011 | | | |
| Catholic Church of America | 501(c)(3) | 2004 | | | |
| Center Church San Diego | 501(c)(3) | 2014 | | | |
| Centers for Spiritual Living | 501(c)(3) | 2014 | | | |
| Centro Cristiano Bethel Icip | 501(c)(3) | 1998 | | | |
| Centro Cristiano Luz Y Salvacion SD Inc | 501(c)(3) | 2025 | | | |
| Centro Cristiano Monte Hebron Inc | 501(c)(3) | 1998 | | | |
| Centro Cristiano Nuevas de Salvacion Inc | 501(c)(3) | 2017 | | | |
| Centro Familiar Cristiano | 501(c)(3) | 1970 | | | |
| Centro Pentecostes Hispano Inc | 501(c)(3) | 2003 | | | 2001-12 |
| Centro de Avivamiento | 501(c)(3) | 1992 | | | |
| Centro de Avivamiento Jesus Rey de Reyes Inc | 501(c)(3) | 2014 | | | |
| Centro de Capacitacion Cristiano | 501(c)(3) | 2025 | | | |
| Chabad Center of University City | 501(c)(3) | 2009 | | | |
| Chabad Jewish Center - Del Mar Inc | 501(c)(3) | 2003 | | | |
| Chabad Mission Valley | 501(c)(3) | 2026 | | | |
| Chabad of Black Mountain Ranch | 501(c)(3) | 2020 | | | |
| Chabad of East County | 501(c)(3) | 2018 | | | |
| Chabad of North Park San Diego | 501(c)(3) | 2026 | | | |
| Chabad of Pacific Beach | 501(c)(3) | 2010 | | | 2024-12 |
| Chabad of Tierrasanta | 501(c)(3) | 2024 | | | |
| Champou Ruckha Vanaram | 501(c)(3) | 2007 | $0 | $508,382 | 2024-12 |
| Chavurat Shir Hayam | 501(c)(3) | 2026 | | | |
| Chinese Church Pastors Fellowshipof San Diego Inc | 501(c)(3) | 2023 | $0 | $0 | 2025-12 |
| Chinese Reformed Church of San Diego | 501(c)(3) | 2014 | | | |
| Chords of Hope Inc | 501(c)(3) | 2024 | $0 | $0 | 2024-12 |
| Christ Centered Church International | 501(c)(3) | 2000 | | | |
| Christ Chapel of North Park San Diego | 501(c)(3) | 1999 | | | |
| Christ Church Universal Inc | 501(c)(3) | 2022 | | | |
| Christ Church of San Diego California | 501(c)(3) | 1998 | | | |
| Christ Church of the Resurrection | 501(c)(3) | 2013 | | | |
| Christ Community Church of San Diego Inc | 501(c)(3) | 2002 | | | |
| Christ the King Catholic Parish in San Diego Ca Real Prop Support Cor | 501(c)(3) | 2019 | | | |
| Christian Church of All Nations | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Christian Citizenship Council | 501(c)(3) | 2012 | $0 | $0 | 2025-12 |
| Christian City Church Mission Bay | 501(c)(3) | 2010 | | | |
| Christian Comic Arts Society | 501(c)(3) | 2009 | $0 | $0 | 2025-12 |
| Christian Life Center of San Diego Inc | 501(c)(3) | 2002 | | | |
| Christs Kingdom Ministries | 501(c)(3) | 1999 | $0 | $0 | 2025-12 |
| Chua Dinh Thanh | 501(c)(3) | 2012 | | | |
| Church 180 | 501(c)(3) | 2020 | | | |
| Church Tsidkenu Inc | 501(c)(3) | 2019 | | | |
| Church of Christ 61St & Division Streets | 501(c)(3) | 2002 | | | |
| Church of Christ On El Cajonblvd | 501(c)(3) | 2004 | | | |
| Church of Divinity | 501(c)(3) | 2001 | | | |
| Church of God International Members San Diego California | 501(c)(3) | 2018 | | | 2018-12 |
| Church of Jesus Christ Yesterday Today and Forever | 501(c)(3) | 2001 | | | |
| Church of Music and Movement | 501(c)(3) | 2026 | | | |
| Church of Wisdom and Peace of Christ | 501(c)(3) | 2025 | | | |
| Church of the Eternal God | 501(c)(3) | 2002 | | | |
| Church of the Loving God | 501(c)(3) | 2017 | | | |
| City Gate Ministry | 501(c)(3) | 2018 | | | |
| City On A Hill Christian Church Inc | 501(c)(3) | 2012 | | | |
| City of Faith | 501(c)(3) | 2015 | | | |
| City of Hope International | 501(c)(3) | 2007 | | | |
| City of Praise Inc | 501(c)(3) | 2011 | | | |
| City of Refuge Church Inc | 501(c)(3) | 1999 | | | |
| Citywalk Christian Church | 501(c)(3) | 2007 | | | |
| Cliffside Church Inc | 501(c)(3) | 2020 | | | |
| Coding Spirit Temple Inc | 501(c)(3) | 2020 | | | |
| Collective San Diego | 501(c)(3) | 2017 | $0 | $0 | 2025-12 |
| Community Missionary Baptist Church | 501(c)(3) | 2023 | | | |
| Congregation Tifereth Israel of San Diego | 501(c)(3) | 2010 | | | |
| Conscious Living Collective | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Contemplative Communications | 501(c)(3) | 1997 | $0 | $0 | 2026-06 |
| Covenant Faith Ministries | 501(c)(3) | 2002 | | | |
| Create Church | 501(c)(3) | 2024 | | | |
| Cross and Crown | 501(c)(3) | 2017 | | | |
| DDR Sanctuary | 501(c)(3) | 2021 | | | |
| Dare To Be A Daniel Foundation | 501(c)(3) | 2026 | | | |
| Darusalaam Foundation | 501(c)(3) | 1999 | | | |
| Declare His Glory Ministries | 501(c)(3) | 2024 | $0 | $0 | 2025-12 |
| Delta Beta Tau | 501(c)(3) | 2023 | $0 | $0 | 2025-12 |
| Dewnamis Ministries Inc | 501(c)(3) | 2000 | $0 | $0 | 2025-12 |
| Dharma Bums | 501(c)(3) | 2018 | | | |
| Dharma Center of Trikaya Buddhism | 501(c)(3) | 2024 | | | |
| Dignity of San Diego | 501(c)(3) | 1976 | $0 | $0 | 2024-12 |
| Dinastia Pentecostal Inc | 501(c)(3) | 2019 | | | |
| Dios La Biblia Y La Familia Inc | 501(c)(3) | 2018 | | | |
| Dioscidence Studios Ministries | 501(c)(3) | 2026 | | | |
| Disciple Community Mission Church | 501(c)(3) | 2014 | | | |
| Divine Grace Neema Ya Mungu Christian Fellowship | 501(c)(3) | 2018 | $0 | $0 | 2025-12 |
| Dodds Family Foundation Inc | 501(c)(3) | 2025 | | $20,000 | 2025-12 |
| Dodeka Network | 501(c)(3) | 2003 | | | |
| East West Christian Outreach Inc | 501(c)(3) | 1988 | $0 | $0 | 2025-12 |
| Ebenezer Church San Diego Inc | 501(c)(3) | 2019 | | | |
| Ebenezer Mission Baptist Church Inc | 501(c)(3) | 1985 | | | |
| El Alfarero Christian Church | 501(c)(3) | 2001 | | | |
| El Dabar Inc | 501(c)(3) | 2016 | | | |
| Elijah Mountain Ministries | 501(c)(3) | 2013 | | | |
| Encompass Ministries | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Ephesians 4 5 Ministries | 501(c)(3) | 2017 | | | |
| Epic Encounters | 501(c)(3) | 2015 | | | |
| Erishalom Inc | 501(c)(3) | 2022 | $0 | $0 | 2025-12 |
| Esperanza for Sons and Daughters | 501(c)(3) | 2026 | | | |
| Essene-Therapeautae Order | 501(c)(3) | 2014 | | | |
| Ethnos Community Church | 501(c)(3) | 2025 | | | |
| Evangelical Formosan Church of San Diego | 501(c)(3) | 2001 | | | |
| Evangelical Methodist Church of San Diego | 501(c)(3) | 2001 | | | |
| Evangelistic Center of Praise | 501(c)(3) | 2005 | | | |
| Exodus United Methodist Church | 501(c)(3) | 2003 | | | |
| Extreme Christian Ministries Inc | 501(c)(3) | 2011 | $0 | $0 | 2024-12 |
| Faith & Freedom Defense Inc | 501(c)(3) | 2010 | $0 | $0 | 2025-12 |
| Faith Hope & Charity Community Church of San Diego | 501(c)(3) | 2011 | | | |
| Faith Hope Love International | 501(c)(3) | 2013 | $0 | $0 | 2025-12 |
| Faith and Outreach | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| Family Life Christian Fellowship of Poway Inc | 501(c)(3) | 2019 | | | |
| Family Revival Church Inc | 501(c)(3) | 2014 | | | |
| Fellowship of Evangelical Filipino American Ministers | 501(c)(3) | 2015 | | | |
| First Baptist Church of San Diego | 501(c)(3) | 2024 | | | 2013-12 |
| First Love California | 501(c)(3) | 2024 | | | |
| Flood-San Diego | 501(c)(3) | 1972 | | | |
| Flourish San Diego | 501(c)(3) | 2013 | | | |
| Fortaleza de Sion | 501(c)(3) | 2018 | | | |
| Forty-Seventh Street Church of God | 501(c)(3) | 1960 | | | |
| Fountain of Life Church of San Diego Ca | 501(c)(3) | 2000 | | | |
| Four Corner Fellowship Church | 501(c)(3) | 2000 | | | |
| Free Churchof God in Christ in Jesus Name | 501(c)(3) | 2014 | | | |
| Freedom Worship Center | 501(c)(3) | 2006 | | | |
| Freewill Missionary Baptist Church | 501(c)(3) | 2017 | | | |
| Fresh Wind Chinese Church of San Diego Inc | 501(c)(3) | 2013 | | | |
| Friends of Divine Mercy | 501(c)(3) | 2022 | $0 | $0 | 2025-06 |
| Friendship Baptist Church of San Diego California | 501(c)(3) | 2010 | | | |
| Fuente de Salvacion San Diego Inc | 501(c)(3) | 2019 | | | |
| GSDMCC Foundation Inc | 501(c)(3) | 2006 | | | |
| Gani Art Center | 501(c)(3) | 1998 | | | |
| Garden Ministries | 501(c)(3) | 1999 | | | |
| Gathering SD | 501(c)(3) | 2015 | | | |
| Gayle Howard Ministries Inc | 501(c)(3) | 2025 | $0 | $0 | 2024-12 |
| Gems of Truth | 501(c)(3) | 2024 | $0 | $0 | 2025-12 |
| Global Church of God | 501(c)(3) | 1993 | | | |
| Global Mission for Indigenous Natio NS and Nature | 501(c)(3) | 2026 | $0 | $0 | 2025-12 |
| Glory Christian Fellow of San Diego | 501(c)(3) | 1999 | | | |
| Glory Faith Christian Fellowship | 501(c)(3) | 2007 | | | |
| God Family Community Ministries | 501(c)(3) | 2024 | | | |
| Gods House of Rest Church | 501(c)(3) | 2011 | | | |
| Gods New Wineskin Church Inc | 501(c)(3) | 2014 | | | |
| Gods Way Church of Deliverance | 501(c)(3) | 2002 | | | |
| Godswell | 501(c)(3) | 2015 | $0 | $0 | 2024-12 |
| Golden Shore SCC | 501(c)(3) | 2024 | | | |
| Golden Thread Spiritualist | 501(c)(3) | 2024 | | | |
| Good News Baptist Church | 501(c)(3) | 2001 | | | |
| Good News San Diego Church | 501(c)(3) | 2026 | | | |
| Good Shepherd Catholic Parish in San Diego Ca Real Prop Support Cor | 501(c)(3) | 2019 | | | |
| Good Voice Fellowship Church | 501(c)(3) | 2006 | | | |
| Grace & Truth Bible Baptist Church Inc | 501(c)(3) | 2018 | | | |
| Grace Chapel of the Valley | 501(c)(3) | 2002 | | | |
| Grace Christian Fellowship- Tierrasanta | 501(c)(3) | 1998 | | | |
| Grace City Church San Diego | 501(c)(3) | 2016 | | | 2025-12 |
| Grace Covenant Christian Church of the Harvest | 501(c)(3) | 2025 | | | |
| Grace Missionary Baptist Church of San Diego California | 501(c)(3) | 2003 | | | |
| Grace Point Church | 501(c)(3) | 2015 | | | 2006-12 |
| Grace Reformed Bible Church of San Diego | 501(c)(3) | 2011 | | | |
| Grace and Hope Fellowship | 501(c)(3) | 2005 | | | |
| Grace of God Ministrys Inc | 501(c)(3) | 2005 | | | |
| Gran Comision Ministries | 501(c)(3) | 2016 | | | |
| Gratefully Blessed Ministries Inc | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| Great Commission Church of God in Christ | 501(c)(3) | 2003 | | | |
| Great Light Presbyterian Church | 501(c)(3) | 2002 | | | |
| Greater Antioch Cogic of San Diego Inc | 501(c)(3) | 2002 | | | |
| Greater Gospel Center Church of God in Christ | 501(c)(3) | 2006 | | | |
| Greater Johnson Missionary Baptist Church | 501(c)(3) | 2004 | | | |
| Greater Love Missionary Baptist Church | 501(c)(3) | 2000 | | | |
| Greater San Diego Muslim Community Center | 501(c)(3) | 2001 | | | |
| Greater Trinity Baptist Church | 501(c)(3) | 2022 | | | |
| Grupo Unidad San Diego | 501(c)(3) | 2024 | | | |
| Grupo de Unidad Cristiana | 501(c)(3) | 2024 | | $123,897 | 2023-12 |
| Gwaneumsa of San Diego | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| HNM Hope News Mission | 501(c)(3) | 2015 | $0 | $0 | 2025-12 |
| HPC | 501(c)(3) | 2000 | | | |
| Hanbit Church | 501(c)(3) | 1995 | | | |
| Hands United for God Inc | 501(c)(3) | 2019 | $0 | $0 | 2023-12 |
| Hanmaum Presbyterian Church of San Diego | 501(c)(3) | 2017 | | | |
| Harmony Christian Church | 501(c)(3) | 2012 | | | |
| Hasson Lifestreams Foundation | 501(c)(3) | 2009 | | $7.9 million | 2024-12 |
| Healing the Nations Ministries | 501(c)(3) | 2008 | $0 | $0 | 2025-12 |
| Heart of God Christian Fellowship | 501(c)(3) | 2009 | | | |
| Heart of God Ministries Inc | 501(c)(3) | 2016 | | | |
| High Noon Ranch Church Ministries Inc | 501(c)(3) | 2017 | $0 | $0 | 2024-12 |
| Higher Praise Christian Fellowship | 501(c)(3) | 2025 | | | |
| Hispanic International Preterist Association USA Inc | 501(c)(3) | 2020 | | | |
| Holy Family Catholic Parish in San Diego Ca Real Property Support | 501(c)(3) | 2018 | | | |
| Holy Hands Church of God in Christ San Diego | 501(c)(3) | 2002 | | | |
| Holy Spirit Catholic Parish in San Diego Ca Real Prop Support Corp | 501(c)(3) | 2019 | | | |
| Home SD Inc | 501(c)(3) | 2025 | | | |
| Honor God Ministries | 501(c)(3) | 2016 | $0 | $0 | 2025-12 |
| Hosanna Mission Church of San Diego | 501(c)(3) | 2008 | | | |
| House of David Church of God in Christ | 501(c)(3) | 2005 | | | |
| House of Grace Outreach Inc | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| House of Grace Worship Center | 501(c)(3) | 2019 | | | |
| House of Prayer Full Gospel Ministry | 501(c)(3) | 2020 | | | |
| Houses of Light of San Diego G12 | 501(c)(3) | 2011 | | | |
| Icon Church | 501(c)(3) | 2010 | | | |
| Idj Saved By Grace | 501(c)(3) | 2025 | | | |
| Iglesia Ancla Inc | 501(c)(3) | 2019 | | | |
| Iglesia Apostolica Fuente de Vida | 501(c)(3) | 2000 | | | |
| Iglesia Apostolica Remanente Escogido SD | 501(c)(3) | 2024 | | | |
| Iglesia Biblica Bautista Sion | 501(c)(3) | 2019 | | | |
| Iglesia Casa de Alabanza Comunidad En Cristo | 501(c)(3) | 2018 | | | |
| Iglesia Centro de Amor | 501(c)(3) | 2018 | | | |
| Iglesia Cristiana Pentecostes Emanuel Inc | 501(c)(3) | 2013 | | | |
| Iglesia Cristiana Pentecostes Esposa Del Cordero Inc | 501(c)(3) | 2015 | | | |
| Iglesia Del Dios Vivo Columna Y Apoyo de La Verdad La Luz Del Mund | 501(c)(3) | 2014 | | | |
| Iglesia Del Evangelio de Cristoleon de Juda | 501(c)(3) | 2008 | | | |
| Iglesia Evangelica Rio de Vida | 501(c)(3) | 2014 | | | |
| Iglesia Familiar | 501(c)(3) | 2010 | | | |
| Iglesia Fuente de Salvacion En San Diego Inc | 501(c)(3) | 2009 | | | |
| Iglesia Nueva Promesa En Cristojesus | 501(c)(3) | 2008 | | | |
| Iglesia Pentecostal Betesda | 501(c)(3) | 2014 | | | |
| Iglesia Pentecostal Unida de Mexico | 501(c)(3) | 2008 | | | |
| Iglesia Plenitud | 501(c)(3) | 2026 | | | |
| Iglesia Unidoe En Cristo | 501(c)(3) | 2014 | | | |
| Iglesia Victoriosa Nuevo Pacto Inc | 501(c)(3) | 2014 | | | |
| Iglesia de Cristo Fuego de Dios | 501(c)(3) | 2025 | | | |
| Iglesia de Cristo K Street | 501(c)(3) | 2011 | | | |
| Iglesia de Cristo Ministerios Llamada Final Inc of San Diego | 501(c)(3) | 2015 | | | |
| Iglesia de Cristo Unidos En Amor Inc | 501(c)(3) | 2013 | | | |
| Iglesia de Dios Pentecostes Rios de | 501(c)(3) | 2009 | | | |
| Iglesia de Jesucristo El Arca de Oro | 501(c)(3) | 2024 | | | |
| Iglesia de Jesucristo Palabra Miel - San Diego | 501(c)(3) | 2019 | | | |
| Iglesia de Jesucristo Palabra-Miel | 501(c)(3) | 2004 | | | |
| Iglesias Cristianas Pentecostales M Ovimiento Mision de Dios Internaci | 501(c)(3) | 2011 | | | |
| Iglesias Vida San Diego Inc | 501(c)(3) | 2016 | | | |
| Iglesias de Restauracion Filial Oceanside | 501(c)(3) | 2001 | | | |
| Imam Ali Ibn Abi Talib Center Inc | 501(c)(3) | 1998 | | | |
| Immaculata Catholic Parish in San Diego Ca Real Prop Support Cor | 501(c)(3) | 2018 | | | |
| Immaculate Conception Catholic Parish in San Diego Ca Real Prop S | 501(c)(3) | 2019 | | | |
| Immanuel Christian Fellowship | 501(c)(3) | 2006 | | | |
| Immanuel Temple Apostolic Church | 501(c)(3) | 1998 | | | |
| Impact San Diego | 501(c)(3) | 2025 | | | |
| Indonesian Christian Fellowship San Diego | 501(c)(3) | 2020 | $0 | $0 | 2025-12 |
| Insight San Diego | 501(c)(3) | 2015 | $0 | $0 | 2025-12 |
| Integrity Christian Fellowship | 501(c)(3) | 2007 | | | |
| International Christian Church of San Diego | 501(c)(3) | 1999 | | | |
| International Foundation of the Seven Stars | 501(c)(3) | 2014 | | $3.2 million | 2025-07 |
| International Soul of Healing Arts Incorporated | 501(c)(3) | 2016 | | | |
| Irvine the Early Church Inc | 501(c)(3) | 2016 | | | |
| Iskcon Cultural Center Inc | 501(c)(3) | 1999 | | | |
| Islamic Center of San Diego | 501(c)(3) | 2014 | | | |
| Islamic Educational Center of San Diego | 501(c)(3) | 2005 | | | |
| Jdo Ministries | 501(c)(3) | 2015 | $0 | $0 | 2025-12 |
| Jehovahs Truth Full Gospel Ministries Inc | 501(c)(3) | 2010 | | | |
| Jerusalem Center for Biblical & Research | 501(c)(3) | 1983 | $0 | $0 | 2025-12 |
| Jesus Burgers Ministries | 501(c)(3) | 2026 | | | |
| Jesus Cares Incorporated | 501(c)(3) | 2014 | $0 | $0 | 2025-09 |
| Jesus Hope Korean Church | 501(c)(3) | 1992 | | | |
| Jesus Oikos Church | 501(c)(3) | 2024 | | | |
| Jesus the Great I Am Church Inc | 501(c)(3) | 2012 | | | |
| Jesusfit Church | 501(c)(3) | 2024 | | | |
| Jigme Lingpa Center | 501(c)(3) | 2005 | $0 | $0 | 2025-12 |
| Joyful Heart Church of New Thought | 501(c)(3) | 2003 | | | |
| Jozen Temple | 501(c)(3) | 2003 | | | |
| Just 1 Evangelism Training | 501(c)(3) | 2020 | $0 | $1,191 | 2024-12 |
| Kaibigan NG Immaculate Conception Major Seminary Sa America | 501(c)(3) | 1994 | $0 | $0 | 2023-12 |
| Karma Dharma Publishing Co Inc | 501(c)(3) | 2009 | $0 | $1 | 2025-12 |
| Kehillat Ahavat Yisrael | 501(c)(3) | 2004 | | | |
| Kidane Mehret Eritrean Tewahedo Orthodox Church in San Diego | 501(c)(3) | 2002 | | | |
| King of Kings Temple Church of God in Christ of San Diego California | 501(c)(3) | 2000 | $0 | $0 | 2025-12 |
| Kingdom Advance Ministries | 501(c)(3) | 2026 | | | |
| Kingdom Culture Inc | 501(c)(3) | 2021 | $0 | $0 | 2024-12 |
| Kingdom Dna Global Ministries | 501(c)(3) | 2026 | | | |
| Kings Cross Church of San Diego | 501(c)(3) | 2026 | | | |
| Koinonia Community Baptist Churchof San Diego | 501(c)(3) | 2007 | | | |
| Korean Young-Nak Presyterian Church Inc | 501(c)(3) | 2005 | | | |
| La Jolla Community Church Inc | 501(c)(3) | 2006 | | | |
| La Nueva Semilla | 501(c)(3) | 2015 | | | |
| Laffaye Brothers Foundation | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Lagoinha San Diego Church | 501(c)(3) | 2025 | | | |
| Lamb Music & Ministries | 501(c)(3) | 1999 | $0 | $0 | 2025-12 |
| Laurel Bible Chapel Inc | 501(c)(3) | 2008 | | | |
| Liberal Rite Catholic Church | 501(c)(3) | 2008 | | | |
| Liberation Crusade Inc | 501(c)(3) | 2023 | $0 | $0 | 2025-12 |
| Life Changing Christian Center | 501(c)(3) | 1998 | | | |
| Life Environmental Welfare Ass | 501(c)(3) | 1995 | $0 | $0 | 2024-12 |
| Life Family Worship International | 501(c)(3) | 2009 | $0 | $0 | 2019-12 |
| Life Rescue Uganda | 501(c)(3) | 2026 | | | |
| Lifepoint Christian Community of San Diego | 501(c)(3) | 2006 | | | |
| Light of THR World Christian Community Church | 501(c)(3) | 1998 | | | |
| Light of the Trinity Trinitarian Marian Spiritual Temple | 501(c)(3) | 1995 | | | |
| Like Our Own | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Linda Vista Second Baptist Church | 501(c)(3) | 2001 | | | |
| Linda Vista Vietnamese Baptist Church | 501(c)(3) | 2007 | | | |
| Little Lilly Outreach Ministry | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Living Epistles Christian Center | 501(c)(3) | 2001 | | | |
| Living Room Foundation Inc | 501(c)(3) | 2019 | | | |
| Living Water Bible Church | 501(c)(3) | 2013 | | | 2015-12 |
| Living Water Church of the Nazarene | 501(c)(3) | 2018 | | | |
| Livingstone Chinese Christian Church of San Diego | 501(c)(3) | 2016 | | | |
| Logan Temple African Methodist Episcopal Zion Church | 501(c)(3) | 2008 | | | |
| Lone Soldier Elite Performance | 501(c)(3) | 2026 | | | |
| Louder Still Worship Inc | 501(c)(3) | 2021 | $0 | $0 | 2023-12 |
| Love Drives Us Inc | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Love of Christ Chrisitan Fellowship | 501(c)(3) | 2016 | | | |
| Love of God International Fellowship | 501(c)(3) | 2022 | | | |
| Lttni | 501(c)(3) | 2024 | $0 | $0 | 2025-12 |
| Luz World Evangelism | 501(c)(3) | 2011 | $0 | $0 | 2025-12 |
| Lydias Daughters Network | 501(c)(3) | 2004 | $0 | $0 | 2025-12 |
| Macedonia Missionary Baptist Church | 501(c)(3) | 2025 | | | |
| Magen Abraham Inc | 501(c)(3) | 2007 | | | |
| Magnificat North County Chapter | 501(c)(3) | 1946 | $0 | $0 | 2026-07 |
| Mahayana Buddhist Society | 501(c)(3) | 2001 | | | |
| Makers Church | 501(c)(3) | 2014 | | | |
| Maranatha Development Foundation | 501(c)(3) | 2014 | | | |
| Mary Magdalene Apostle Catholic Community | 501(c)(3) | 2006 | | | |
| Masjid Al-Ansar | 501(c)(3) | 2001 | | | |
| Masjidul Taqwa | 501(c)(3) | 2007 | | | |
| McNamara Triplet Foundation | 501(c)(3) | 2025 | | $471,300 | 2024-12 |
| Mega Eagle Wings | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Mexico Ministries & Mission | 501(c)(3) | 2007 | | | |
| Mierafe Kidusan Abune Teklehaimanot Ethiopian Orthodox Tewahido Churc | 501(c)(3) | 2014 | | | |
| Ministerio de Restauracion Mundial | 501(c)(3) | 2016 | | | |
| Ministerios Internacionales Maranatha | 501(c)(3) | 2024 | $0 | $0 | 2025-12 |
| Ministerios de Obreros de Cristo Inc | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Mira Mesa Bible Baptist Church Inc | 501(c)(3) | 2014 | | | |
| Mission Bay International Christian Church | 501(c)(3) | 2012 | | | |
| Mission Beach Christian Fellowship | 501(c)(3) | 2020 | | | |
| Mission Church Beyond | 501(c)(3) | 2022 | | | |
| Mission Focused | 501(c)(3) | 2012 | $0 | $0 | 2024-06 |
| Mission San Diego de Alcala Catholic Parish in San Diego Ca Re | 501(c)(3) | 2018 | | | |
| Mission Valley Christian Fellowship | 501(c)(3) | 1996 | | | |
| Mission Village Christian Fellowship | 501(c)(3) | 2009 | | | |
| Mission de Dios Mount Olive International Inc | 501(c)(3) | 2012 | | | |
| Mobeen | 501(c)(3) | 2025 | | | |
| Mobile Ministers | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| Momin Services | 501(c)(3) | 1996 | | | 2008-12 |
| Monument of Love Fellowship Christian Center of San Diego | 501(c)(3) | 2003 | | | |
| Morning Star Christian Fellowship | 501(c)(3) | 2000 | | | |
| Most Excellent Way-Mexico Inc | 501(c)(3) | 2006 | $0 | $0 | 2025-12 |
| Mount Erie Baptist Church | 501(c)(3) | 2011 | | | |
| Mount Olive Baptist Church of San D Iego California | 501(c)(3) | 2026 | | | |
| Mount Pisgah Baptist Church of San Diego California | 501(c)(3) | 2005 | | | |
| Movement of the Vietnamese Laity in Diaspora | 501(c)(3) | 2012 | $0 | $0 | 2025-12 |
| Mt Moriah Christian Church | 501(c)(3) | 2015 | | | |
| Mt Sinai Christian Fellowship | 501(c)(3) | 2011 | | | |
| Mujer Tu No Estas Sola Sin Fronteras Inc | 501(c)(3) | 2024 | $0 | $0 | 2023-12 |
| Muslim Leadership Council of San Diego Inc | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| Nam Christian Community | 501(c)(3) | 2007 | | | |
| Nancy Fenn Memorial Scholarship Inc | 501(c)(3) | 2015 | $0 | $0 | 2024-12 |
| Needs and Deeds | 501(c)(3) | 2000 | $0 | $0 | 2025-12 |
| Neighbors Church | 501(c)(3) | 2019 | | | |
| Nejashi Islamic Community of San Diego Inc | 501(c)(3) | 2015 | | | |
| New Beginnings Church | 501(c)(3) | 2002 | | | |
| New Beginnings Church of God in Christ | 501(c)(3) | 2013 | | | |
| New Creation United Church of Christ | 501(c)(3) | 1996 | | | |
| New Day Community Church | 501(c)(3) | 2023 | | $5,000 | 2023-12 |
| New Gods | 501(c)(3) | 2023 | | | |
| New Ground Ministries Inc | 501(c)(3) | 2022 | | | |
| New Hope Friendship Baptist Church | 501(c)(3) | 2005 | | | |
| New Life Christian Covenant Church | 501(c)(3) | 2014 | | | |