| Glide Foundation | 501(c)(3) | 2009 | $28.3 million | $54.7 million | 2025-06 |
| Tawonga Jewish Community Corporation | 501(c)(3) | 1996 | $11.3 million | $26.7 million | 2024-12 |
| Libitzky Family Foundation | 501(c)(3) | 2001 | $6.7 million | $17.9 million | 2025-06 |
| Chevra Kadisha-Sinai Memorial Chapel | 501(c)(3) | 1935 | $6.2 million | $28 million | 2024-12 |
| Khyentse Foundation | 501(c)(3) | 2002 | $5.4 million | $52.6 million | 2025-06 |
| Crazy Love Ministries | 501(c)(3) | 2015 | $4.9 million | $8.5 million | 2024-12 |
| United Religions | 501(c)(3) | 1996 | $3.5 million | $16.2 million | 2024-12 |
| Rimon Club Z Inc | 501(c)(3) | 2014 | $2.9 million | $2.1 million | 2025-06 |
| Jewish Learningworks | 501(c)(3) | 1935 | $2.2 million | $6.9 million | 2025-06 |
| International Hotel Senior Housing Inc | 501(c)(3) | 1996 | $1.7 million | $16.4 million | 2025-12 |
| Stratum | 501(c)(3) | 2021 | $1.6 million | $696,401 | 2025-06 |
| Episcopal Impact Fund | 501(c)(3) | 2000 | $1.3 million | $7.6 million | 2025-12 |
| Glide Community Church | 501(c)(3) | 2018 | $1.3 million | $1 million | 2025-06 |
| Narrative Magazine Inc | 501(c)(3) | 2005 | $885,753 | $996,923 | 2024-12 |
| Fullness in Christ Fellowship | 501(c)(3) | 2009 | $848,692 | $2.5 million | 2025-12 |
| Irving and Varda Rabin Foundation | 501(c)(3) | 2000 | $737,656 | $2.3 million | 2025-06 |
| Faithful Fools Street Ministry | 501(c)(3) | 2000 | $686,643 | $1.1 million | 2025-12 |
| Acts 17 | 501(c)(3) | 2025 | $598,419 | $264,556 | 2025-12 |
| Center for Church Innovation | 501(c)(3) | 2023 | $533,695 | $336,019 | 2025-08 |
| Joseph Pedott Perpetual Endowment Trust | 501(c)(3) | 2004 | $456,609 | $11.1 million | 2025-06 |
| Interfaith Center at the Presidio | 501(c)(3) | 1996 | $430,680 | $2.2 million | 2025-06 |
| Neighborhood Baptist Church | 501(c)(3) | 2009 | $411,407 | $3 million | 2024-12 |
| Gurdjieff Foundation of California | 501(c)(3) | 1962 | $355,240 | $3 million | 2025-08 |
| Matthew Fox Legacy Project | 501(c)(3) | 2015 | $335,723 | $180,817 | 2024-12 |
| Proxima Partners Inc | 501(c)(3) | 2025 | $313,846 | $17,094 | 2025-12 |
| Quong Ming Buddhism & Taoism Society of San Francisco | 501(c)(3) | 1977 | $312,620 | $3.2 million | 2025-12 |
| Iglesia El Espiritu Santo Church | 501(c)(3) | 1998 | $310,887 | $1.9 million | 2024-12 |
| Neos Initiative | 501(c)(3) | 2022 | $294,392 | $173,970 | 2025-12 |
| Gather Ministries Inc | 501(c)(3) | 2014 | $272,887 | $1.5 million | 2025-12 |
| Amigos de San Elias Inc | 501(c)(3) | 2024 | $270,269 | $445,350 | 2024-12 |
| The Serra Schools | 501(c)(3) | 2026 | $269,966 | $0 | 2025-08 |
| Dzokden | 501(c)(3) | 2022 | $259,762 | $365,565 | 2025-12 |
| Mastery Foundation | 501(c)(3) | 1986 | $257,834 | $253,032 | 2025-12 |
| Greater Hope Life Change Center | 501(c)(3) | 2022 | $244,675 | $151,026 | 2025-12 |
| Soto Zen Buddhism International Center | 501(c)(3) | 2004 | $240,108 | $40,977 | 2026-03 |
| Western States Fellowship | 501(c)(3) | 1980 | $234,426 | $147,543 | 2024-12 |
| Dignity San Francisco Inc | 501(c)(3) | 1974 | $222,090 | $1.2 million | 2025-12 |
| Kingdom Rice | 501(c)(3) | 2017 | $183,529 | $153,928 | 2024-12 |
| Cultivate Pastors and Churches Inc | 501(c)(3) | 2023 | $171,602 | $153,628 | 2024-12 |
| Episcopal Network for Stewardship Inc | 501(c)(3) | 1998 | $151,723 | $48,571 | 2025-12 |
| Second Union Missionary Baptist Church | 501(c)(3) | 2025 | $151,337 | $6,753 | 2025-12 |
| Northern California Uu Camps and Conferences | 501(c)(3) | 2006 | $142,497 | $28,408 | 2025-12 |
| San Francisco Buddist Center Triratna | 501(c)(3) | 1995 | $137,505 | $812,259 | 2025-06 |
| Al Sabeel A California Religious Co Rporation | 501(c)(3) | 2003 | $123,177 | $1.1 million | 2025-12 |
| Sunflower Organization Inc | 501(c)(3) | 2022 | $116,638 | $47,155 | 2024-12 |
| The Servants Ministries | 501(c)(3) | 2023 | $116,130 | $143,857 | 2025-12 |
| San Francisco Dharma Collective | 501(c)(3) | 2019 | $115,095 | $70,564 | 2025-12 |
| Iglesia de Restauracion Betel | 501(c)(3) | 2024 | $115,080 | $15,726 | 2020-12 |
| Alice M R Griffin Fund | 501(c)(3) | 1963 | $107,990 | $1.6 million | 2024-12 |
| Vasudharayana | 501(c)(3) | 2020 | $101,192 | $762,829 | 2024-12 |
| Pray the Bay Area | 501(c)(3) | 2023 | $83,451 | $36,224 | 2024-12 |
| Holy Ghost Service Center | 501(c)(3) | 2007 | $75,170 | $829,240 | 2025-12 |
| Ignatian Center | 501(c)(3) | 2024 | $73,106 | $41,762 | 2025-12 |
| Iglesia de Cristo MC Fuente de Vida Inc | 501(c)(3) | 2013 | $65,121 | $0 | 2021-12 |
| Lin Du Temple | 501(c)(3) | 1998 | $50,989 | $1.1 million | 2026-07 |
| Wong Tai Sen Temple & Services Inc | 501(c)(3) | 2025 | $49,559 | $4,861 | 2025-12 |
| Ywam Nations2nations | 501(c)(3) | 2017 | $35,849 | $30,373 | 2024-12 |
| Casa de Oracion Rey de Reyes Senor de Senores Inc | 501(c)(3) | 2016 | $31,978 | $2,331 | 2025-12 |
| Sanctuary Missionaries of Divine Mercy | 501(c)(3) | 2026 | $25,000 | $0 | 2025-12 |
| Zen Foundation | 501(c)(3) | 2011 | $20,154 | $830 | 2025-04 |
| Knights of St Francis of Assisi | 501(c)(3) | 2010 | $18,257 | $5,645 | 2025-12 |
| Taoist Association of America C/o Lew & Fong | 501(c)(3) | 1980 | $6,596 | $18,067 | 2025-03 |
| The L&R Lawrence Family Foundation | 501(c)(3) | 2004 | $3,459 | $1.4 million | 2025-06 |
| Zen Without Borders | 501(c)(3) | 2024 | $2,000 | $2,000 | 2023-12 |
| Dayspring Community Partners Inc | 501(c)(3) | 1996 | $700 | $156,144 | 2024-12 |
| Piazza Saint Francis A Poet S Plaza Inc | 501(c)(3) | 2014 | $28 | $16,254 | 2025-12 |
| 19TH Ave Japanese Baptist Church | 501(c)(3) | 1997 | | | |
| 99 Church of San Francisco | 501(c)(3) | 2020 | | | |
| Abrahamic House of Worship | 501(c)(3) | 2010 | | | |
| Adath Israel | 501(c)(3) | 2002 | | | |
| Addis Kidan Ethiopian and Eritrean Church of San Francisco | 501(c)(3) | 2012 | | | |
| Al Ajwah Islamic Dawah Learning Center Inc | 501(c)(3) | 2009 | $0 | $0 | 2025-12 |
| All Saints Company | 501(c)(3) | 2008 | | $153,630 | 2024-12 |
| All Saints Foundation | 501(c)(3) | 2015 | $0 | $0 | 2025-12 |
| Anjaman Fidayan Rasool | 501(c)(3) | 2000 | $0 | $0 | 2025-12 |
| Asa Missionary Baptist Church Inc | 501(c)(3) | 2000 | | | |
| Aslan Housing Impact | 501(c)(3) | 2026 | | | |
| Association for Advancement of Buddhist Culture | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Association of Tao Development | 501(c)(3) | 2004 | | | |
| Awakened Living | 501(c)(3) | 2013 | | | |
| BMS International | 501(c)(3) | 2021 | | | |
| Bay Doorae Community Church | 501(c)(3) | 2008 | | | |
| Bay Wide Young Adults | 501(c)(3) | 2025 | $0 | $0 | 2025-09 |
| Be All Church | 501(c)(3) | 1999 | | | |
| Because Justice Matters Inc | 501(c)(3) | 2026 | | | |
| Believers House of Victory Inc | 501(c)(3) | 2006 | | | |
| Bethel On the Bay Community Inc | 501(c)(3) | 2026 | | | |
| Bnai Noah Institute-Shalom Spiritual Resources | 501(c)(3) | 2004 | | | |
| Bodhi Path Buddhist Center of San Francisco | 501(c)(3) | 2015 | | | |
| Bool Kwang Sa Buddhist Temple | 501(c)(3) | 1996 | | | |
| Bread of Life Christian Church Insan Francisco | 501(c)(3) | 2009 | | | |
| Bread of Life Pentecostal Worship Center | 501(c)(3) | 2004 | | | |
| Buddhis Foundation Diamond Way of the Karma Kagyu Lineage | 501(c)(3) | 2009 | | | |
| Buddhist True Bodhi Association | 501(c)(3) | 2020 | | | |
| CSL Ashbury Heights | 501(c)(3) | 2014 | | | |
| Calamus | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| California State Baptist Convention Inc | 501(c)(3) | 2008 | $0 | $0 | 2025-12 |
| Calvary Baptist Church | 501(c)(3) | 2018 | | | |
| Canaan Lutheran Church | 501(c)(3) | 1941 | | | 2006-12 |
| Canvas Church of San Francisco Inc | 501(c)(3) | 2019 | | | |
| Celebration Development Corporation | 501(c)(3) | 2007 | $0 | $0 | 2025-12 |
| Center for Faith and Justice | 501(c)(3) | 2026 | | | |
| Centro Familiar Roca de Salvation de San Francisco Inc | 501(c)(3) | 2016 | | | 2009-12 |
| Chabad Student Center Inc | 501(c)(3) | 2013 | | | |
| Chabad of Central Marin | 501(c)(3) | 2020 | | | |
| Chabad of Cole Valley | 501(c)(3) | 2011 | | | |
| Chabad of Noe Valley | 501(c)(3) | 2002 | | | |
| Chabad of the Neighborhood | 501(c)(3) | 2021 | | | |
| Chan Buddha Temple | 501(c)(3) | 2026 | | | |
| China Songshan Shaolin Temple San Francisco USA Inc | 501(c)(3) | 2006 | | | |
| Chinese Christian Family Conference | 501(c)(3) | 2024 | $0 | $0 | 2023-12 |
| Chinese Christian Ministerial Prayer Fellowship of Bay Area | 501(c)(3) | 2007 | $0 | $0 | 2025-12 |
| Chinese Christian Union of San Francisco | 501(c)(3) | 2000 | $0 | $0 | 2025-12 |
| Chinese Lutherans in Mission Building | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| Chozen-Ji Betsuin of California | 501(c)(3) | 1998 | | | |
| Christ Church of San Francisco | 501(c)(3) | 2019 | | | |
| Christian Community in North America Central Fund | 501(c)(3) | 1997 | | | |
| Christian Family Gospel Ministries | 501(c)(3) | 2022 | $0 | $0 | 2025-12 |
| Chunbukyo Church of San Francisco Inc | 501(c)(3) | 1996 | | | |
| Church On the Go USA | 501(c)(3) | 2024 | $0 | $0 | 2024-12 |
| Church of Endzeit Inc | 501(c)(3) | 2025 | | | |
| Church of Sweden San Francisco | 501(c)(3) | 2010 | | | |
| Church of the Truth of San Francisco | 501(c)(3) | 2009 | | | |
| Citizens Church of San Francisco | 501(c)(3) | 2017 | | | |
| City Life Church San Francisco | 501(c)(3) | 2014 | | | |
| Clear Water Sangha | 501(c)(3) | 2008 | | | |
| Committee To Save St Brigid Church | 501(c)(3) | 1995 | $0 | $0 | 2025-12 |
| Common Table | 501(c)(3) | 2017 | | | |
| Community of St Francis Inc | 501(c)(3) | 2007 | | | |
| Companions of Dorothy the Worker Inc | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| Concord Missionary Baptist Church | 501(c)(3) | 1987 | | | |
| Congregation Anshey Sfard | 501(c)(3) | 2001 | | | |
| Congregation Beth Sholom San Francisco | 501(c)(3) | 2002 | | | |
| Congregation Chevra Thilim | 501(c)(3) | 1986 | | | |
| Congregation for Sacred Practices | 501(c)(3) | 2022 | | | |
| Cornerstone Trinity Baptist Church | 501(c)(3) | 1972 | | | |
| Crazy Love Studios | 501(c)(3) | 2026 | | | |
| Cristo Viene - Efecio 4 11 | 501(c)(3) | 2017 | | | |
| Crossings Collective | 501(c)(3) | 2026 | | | |
| Daring Faith Celebration Centre | 501(c)(3) | 2018 | | | |
| Daring Faith Celebration Foundation | 501(c)(3) | 2018 | | | |
| Dechen Yulokope Shedupling Tibetanbuddhist Center | 501(c)(3) | 2006 | $0 | $0 | 2025-12 |
| Dharma Treasury Study Center Inc | 501(c)(3) | 2003 | $0 | $0 | 2025-12 |
| Dharmawheels Foundation | 501(c)(3) | 2013 | $0 | $0 | 2025-12 |
| Diocese of Chaplaincy Service | 501(c)(3) | 2014 | | | |
| Divine House of God | 501(c)(3) | 2003 | $0 | $0 | 2024-12 |
| Dragons Leap | 501(c)(3) | 2012 | | | |
| El Santo de Israel | 501(c)(3) | 2004 | | | |
| Elderflower Womenspirit Festival | 501(c)(3) | 2024 | $0 | $0 | 2025-09 |
| Emerge Global | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Emmanuel Teaching Mission | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Epic Church San Francisco | 501(c)(3) | 2018 | | | |
| Eucharist | 501(c)(3) | 2011 | | | |
| Evergreen Baptist Church | 501(c)(3) | 2010 | | | |
| Experience Church | 501(c)(3) | 2009 | | | |
| Faith Christian Center of San Francisco | 501(c)(3) | 2011 | | | |
| Faith Tabernacle United Pentecostal Church of San Francisco | 501(c)(3) | 1996 | | | |
| Faithful Presbyterian Church | 501(c)(3) | 2019 | | | |
| Fan Yum Buddhist Temple | 501(c)(3) | 2002 | | | |
| Fathers House San Francisco | 501(c)(3) | 2018 | | | |
| Finding Fellowship Inc | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| First United Lutheran Church | 501(c)(3) | 1996 | | | |
| First Universal Congregation of Saint Agnes of Rome | 501(c)(3) | 2016 | | | |
| Fo-Un Buddhist Temple | 501(c)(3) | 1995 | | | |
| Foundation for Ancient Humanities | 501(c)(3) | 2014 | $0 | $0 | 2026-03 |
| Foundation of the Sacred Stream | 501(c)(3) | 2003 | | | 2009-12 |
| Fred Maytag Family Foundation | 501(c)(3) | 1996 | | $57.9 million | 2025-12 |
| Freedom in Christ Evangelical Church of San Francisco California | 501(c)(3) | 1998 | | | |
| Gaganananda Mission | 501(c)(3) | 2020 | $0 | $0 | 2025-12 |
| Good Methodist Church | 501(c)(3) | 1999 | | | 2014-12 |
| Grace Community Church of San Francisco | 501(c)(3) | 2010 | | | |
| Grace Witness Christian Church | 501(c)(3) | 1999 | | | |
| Gratia Presbyterian Church | 501(c)(3) | 2010 | | | 2023-12 |
| Greater Mount Sinai Missionary Baptist Church Inc | 501(c)(3) | 2006 | | | |
| Greater New Mount Enon Missionary Baptist Church of S F Ca | 501(c)(3) | 1999 | | | |
| Greek Orthodox Metropolis of San Francisco | 501(c)(3) | 2008 | | | |
| Greenhouse USA | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Greenwood University | 501(c)(3) | 2018 | $0 | $0 | 2025-12 |
| Guru Ram Das Ashram Inc | 501(c)(3) | 2011 | | | |
| Guy and Louise Condrott Scholarship Fund Inc | 501(c)(3) | 1996 | $0 | $0 | 2025-03 |
| Hand of Help Ministry | 501(c)(3) | 2021 | | | |
| Hands for the Littles in USA | 501(c)(3) | 2021 | $0 | $623 | 2025-12 |
| Hokke Shu Buddist Church | 501(c)(3) | 2012 | $0 | $0 | 2024-12 |
| Hope for the Second Generation | 501(c)(3) | 2021 | $0 | $0 | 2023-12 |
| Hua-Zang Si | 501(c)(3) | 2005 | | | |
| I-Kuan Tao Foundation of America | 501(c)(3) | 1995 | | | |
| Iamspiritalive | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| Iglesia Apostolica La Fe Y La Gracia | 501(c)(3) | 1998 | | | |
| Iglesia Arca de Dios A-G | 501(c)(3) | 2015 | | | |
| Iglesia Cristiana No Temas Que Yo Estoy Contigo | 501(c)(3) | 2003 | $0 | $51,303 | 2025-06 |
| Iglesia Cristiana Pasos de Fe | 501(c)(3) | 2019 | | | |
| Iglesia Cristo Es La Roca Aic | 501(c)(3) | 2017 | | | |
| Iglesia Impacto Pentecostes | 501(c)(3) | 2019 | $0 | $0 | 2023-12 |
| Iglesia Jesus El Mesias San Francisco Inc | 501(c)(3) | 2024 | | | |
| Iglesia Pentecostal Tiempo de Restauracion Inc | 501(c)(3) | 2021 | | | |
| Iglesia Pentecostal de Restauracion Y Sanidad La Novia Del Cordero | 501(c)(3) | 2024 | $0 | $0 | 2024-12 |
| Iglesia Pentecostes Dios Es Amor En California Inc | 501(c)(3) | 2020 | | | |
| Iglesia Pentecostes Rios de Agua Viva San Francisco Inc | 501(c)(3) | 2025 | | | |
| Iglesia Y Santuario La Voz de Dios Y Jesucristo Inc | 501(c)(3) | 2025 | | | |
| Iglesia de Cristo El Camino | 501(c)(3) | 2004 | | | |
| Iglesia de Cristo Ministerios Cosecha Inc | 501(c)(3) | 1998 | | | |
| Iglesia de Cristo Nueva Vision Internacional | 501(c)(3) | 2010 | | | |
| Iglesia de Cristo Torre Fuerte Inc | 501(c)(3) | 2009 | | | |
| Iglesia de Jesucristo Restauracion | 501(c)(3) | 2011 | | | |
| Ikon Christian Community | 501(c)(3) | 2009 | | | |
| Imani Christian Fellowship Ministries | 501(c)(3) | 2009 | | | |
| Immanuel Mongolian Christian Church of San Francisco | 501(c)(3) | 2007 | | | |
| International Buddhism Sangha Association | 501(c)(3) | 2001 | | | |
| International Center of Revival MC | 501(c)(3) | 2020 | | | |
| International House of Prayer | 501(c)(3) | 2006 | | | |
| International Mahayana Institute | 501(c)(3) | 2009 | | | |
| Isaiah 58 7 Project | 501(c)(3) | 2006 | | | |
| James Memorial Church of God in Christ | 501(c)(3) | 2024 | | | |
| James Trumbo-Forerunner Ministries | 501(c)(3) | 2003 | $0 | $0 | 2025-12 |
| Japanese American Religious Federation | 501(c)(3) | 1971 | $0 | $0 | 2025-12 |
| Jesus Christ Son of God Christian Church | 501(c)(3) | 2011 | | | |
| Jesus Miracle Crusade Intl Ministry Under Evangelist Wilde Almeda Inc | 501(c)(3) | 2003 | | | |
| Jews for Fun Organization Inc | 501(c)(3) | 2012 | $0 | $0 | 2024-12 |
| Jodo Shinshu International Office | 501(c)(3) | 2020 | | $6.6 million | 2025-03 |
| Joseph Bryant Ministries Inc | 501(c)(3) | 2021 | $0 | $0 | 2025-12 |
| Joy of All Joys Mission | 501(c)(3) | 2021 | | | |
| Kadampa Meditation Center San Francisco | 501(c)(3) | 2000 | | | |
| Kehillahsf | 501(c)(3) | 2012 | $0 | $0 | 2024-12 |
| Keneset Halev-Community of the Heart | 501(c)(3) | 2015 | $0 | $0 | 2026-02 |
| Kidus Michael Eritrean Orthodox Church of San Francisco | 501(c)(3) | 2016 | $0 | $0 | 2024-12 |
| Kitchen Slow Down Jew Up | 501(c)(3) | 2012 | | | |
| Korean Christian Church of San Francisco | 501(c)(3) | 1997 | | | |
| Korean Lifehouse Covenant Church San Fransisco Ca | 501(c)(3) | 1975 | | | |
| Kpyusa | 501(c)(3) | 2020 | | | |
| La Iglesia de Los Extranjeros Church of the Sojourners | 501(c)(3) | 1995 | | | |
| Lake Merced Church of Christ | 501(c)(3) | 1972 | | | |
| Latvian Evangelical Lutheran Church of Northern California | 501(c)(3) | 2004 | | | |
| Lawkanartha Monastery | 501(c)(3) | 2011 | | | |
| Life Bridge Fellowship | 501(c)(3) | 2013 | | | |
| Life Runners Fellowship | 501(c)(3) | 2025 | | | |
| Lifepoint Church of San Francisco Inc | 501(c)(3) | 2014 | | | |
| Lion of Judah Ministries | 501(c)(3) | 2011 | $0 | $0 | 2026-03 |
| Little Angels Music Ministries | 501(c)(3) | 2015 | $0 | $0 | 2025-06 |
| Living Water Fellowship | 501(c)(3) | 2002 | | | |
| Lost Coin Development | 501(c)(3) | 2010 | | | |
| Lotusseed Dharma Society | 501(c)(3) | 2005 | | | |
| MJ Redmond Ministries Inc | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| Macedonia Missionary Baptist Church | 501(c)(3) | 2005 | | | |
| Maha Bodhi Zen Center | 501(c)(3) | 2010 | | | |
| Maitreya Great Tao Hong Kong Organization Limited | 501(c)(3) | 2002 | | | |
| Maureene Bass Ministries | 501(c)(3) | 2008 | | | |
| Meeting Halls Inc | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| Ming Tsu Temple | 501(c)(3) | 2015 | | | |
| Minifterios de Restauracion El Alsarero Inc | 501(c)(3) | 2009 | | | |
| Ministerio Casa de Restauracion Cosecha | 501(c)(3) | 2023 | | | |
| Ministerio Iglesia Jesucristo Es El Senor | 501(c)(3) | 2020 | | | |
| Ministerio Internacional Jesus El Buen Pastor Inc | 501(c)(3) | 2013 | | | |
| Ministerio de Restauracion Jesucristo Es El Senor | 501(c)(3) | 2025 | | | |
| Ministerios Ebenezer Norte America | 501(c)(3) | 2026 | | | |
| Ministerios Restauracion Casa de Dios Inc | 501(c)(3) | 2016 | | | |
| Ministry of Presence Institute | 501(c)(3) | 2015 | $0 | $0 | 2025-12 |
| Mishalom USA Inc | 501(c)(3) | 2025 | | | |
| Mision Cristiana Monte de Victoria Inc | 501(c)(3) | 2022 | | | |
| Mision Cristiana Pentecostes He Aqui El Cordero de Dios | 501(c)(3) | 2023 | | | |
| Mission Minyan | 501(c)(3) | 2006 | | | |
| Monte Sinai Inglesia de Dios | 501(c)(3) | 2017 | | | |
| Moon Mountain Sangha Inc | 501(c)(3) | 2007 | $0 | $0 | 2025-12 |
| Mount Vernon Missionary Baptist Church | 501(c)(3) | 2005 | | | |
| Msit - Instituto Teologico | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| Mt Zion Baptist Church | 501(c)(3) | 2026 | | | |
| Nation Takers Ministries | 501(c)(3) | 2010 | | | |
| Neary Lagoon Inc | 501(c)(3) | 1996 | $0 | $0 | 2024-12 |
| Network of Lovingkindness -A Not for Profit Foundation | 501(c)(3) | 2006 | | | |
| Neuma USA Inc | 501(c)(3) | 2024 | | | |
| New City Church Oakland | 501(c)(3) | 2021 | | | |
| New Greater Prosperity Community Baptist Church | 501(c)(3) | 1999 | | | |
| New Life Bible Fellowship | 501(c)(3) | 1965 | | | |
| New Life Chinese Lutheran Church | 501(c)(3) | 1941 | | | |
| New Life Christian Fellowship | 501(c)(3) | 1997 | | | |
| New Life Fellowship Baptist Church of San Francisco | 501(c)(3) | 2002 | | | |
| New North Church Inc | 501(c)(3) | 2017 | | | |
| Northern California Buddhists Union | 501(c)(3) | 2025 | | | |
| Norwegian Seamens Church | 501(c)(3) | 2009 | | | |
| Open Source Church | 501(c)(3) | 2019 | | | |
| Or Shalom Jewish Community | 501(c)(3) | 2014 | | | 2025-06 |
| Order of St Georges Horse | 501(c)(3) | 2025 | $0 | $0 | 2026-06 |
| Order of the Beloved Corp | 501(c)(3) | 2025 | | | |
| Original Founders of the 1St Samoan Congregational Ucc of the Bay Area | 501(c)(3) | 1998 | | | |
| Pacific Center for Spiritual Formation | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| Pacific Coast Association of the New Jerusalem Swedenborgian | 501(c)(3) | 2007 | | | 2006-12 |
| Pentecostal Church Alpha Y Omega | 501(c)(3) | 2017 | | | |
| Perazim Christian Liberty Bible Church | 501(c)(3) | 2001 | | | |
| Prayingsite Inc | 501(c)(3) | 2022 | | | |
| RTJ Ministries | 501(c)(3) | 2015 | $0 | $0 | 2025-12 |
| Radiance Christian Church | 501(c)(3) | 2012 | | | |
| Readi Ministries International | 501(c)(3) | 2016 | $0 | $0 | 2024-12 |
| Reality San Francisco Church | 501(c)(3) | 2012 | | | |
| Realm of Blessings Ministries Inc | 501(c)(3) | 2004 | | | |
| Redeemer Community Church | 501(c)(3) | 2003 | | | |
| Redemption Church San Francisco | 501(c)(3) | 2012 | | | |
| Religio Numino | 501(c)(3) | 2024 | | | |
| Resurrected Christ Missionary Baptist Church | 501(c)(3) | 2009 | | | |
| Rising Phoenix Temple Inc | 501(c)(3) | 2025 | | | |
| Rock of Ages Church Baptist Church of the City | 501(c)(3) | 2013 | | | |
| Russian Speaking Jewish Community of San Francisco Bay Area | 501(c)(3) | 2005 | | | |
| Rust Belt Zen Inc | 501(c)(3) | 2020 | $0 | $0 | 2025-12 |
| SF Into Korean Church | 501(c)(3) | 2017 | | | |
| SF No Limits Worship Center | 501(c)(3) | 2019 | | | |
| SHG Foundation | 501(c)(3) | 2000 | | $868,795 | 2024-12 |
| Sacred Plant Alliance | 501(c)(3) | 2024 | | | |
| Sacred Sacraments Ministry | 501(c)(3) | 2022 | $0 | $0 | 2024-12 |
| Sai IIV Inc | 501(c)(3) | 2024 | | | |
| Saint Nicholas Russian Orthodox Cathedral of Moscow Patriarchate | 501(c)(3) | 2017 | | | |
| Saint Paul Tabernacle Baptist Church | 501(c)(3) | 2015 | | | |
| San Fran Dhammaram Temple | 501(c)(3) | 2003 | | | |
| San Francisco Bay-Area Chinese Bible Conference | 501(c)(3) | 2012 | $0 | $0 | 2025-12 |
| San Francisco Community Church of God of Prophecy Inc | 501(c)(3) | 2010 | | | |
| San Francisco Dharma Center | 501(c)(3) | 2017 | | | |
| San Francisco Insight Meditation Community | 501(c)(3) | 2023 | | | |
| San Francisco Korean American Presbyterian Church | 501(c)(3) | 1999 | $0 | $0 | 2022-12 |
| San Francisco Korean Good News Church | 501(c)(3) | 1995 | | | |
| San Francisco Lighthouse | 501(c)(3) | 2004 | | | |
| San Francisco Mikvah | 501(c)(3) | 2023 | $0 | $0 | 2025-08 |
| San Francisco Senior Mission Church | 501(c)(3) | 2000 | | | |
| San Francisco True Light Methodist Church | 501(c)(3) | 2002 | | | |
| San Francisco Vietnamese Baptist Church | 501(c)(3) | 1997 | | | |
| San Francisco Zen Center | 501(c)(3) | 2015 | | | 2001-04 |
| Schneerson Center Inc | 501(c)(3) | 2012 | | | |
| Second Wind City Church | 501(c)(3) | 2003 | | | |
| Servant Phinsee International Ministries | 501(c)(3) | 2025 | | | |
| Sfavcf Inc | 501(c)(3) | 2001 | | | |
| Shekinah Christian Fellowship of San Francisco | 501(c)(3) | 2000 | | | |
| Shu Oak Zen | 501(c)(3) | 2019 | $0 | $0 | 2024-12 |
| Sian Tien Dao Yuan | 501(c)(3) | 2004 | | | |
| Society of Our Lady of Guadalupe | 501(c)(3) | 1997 | | | |
| Society of St Vincent de Paul District Council of San Francisco | 501(c)(3) | 2025 | | | |
| Sophia in Trinity | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| Spirit Shines Christian Ministries Inc | 501(c)(3) | 2022 | $0 | $0 | 2024-12 |
| St Francis Church of Christ | 501(c)(3) | 2014 | | | |
| St George Ethiopian Orthodox Tewahedo Church | 501(c)(3) | 2019 | | | |
| St Ignatius Church | 501(c)(3) | 1946 | | | |
| St Peter the Aleut Orthodox Church Inc | 501(c)(3) | 1995 | | | |
| St Thomas Anglican Church Inc | 501(c)(3) | 2017 | | | |
| St Xenia of Petersburg Rus Orth Church | 501(c)(3) | 2004 | | | |
| Sufi Village International | 501(c)(3) | 2003 | | | |
| Sunday Afternoon Fellowship | 501(c)(3) | 2009 | | | |
| Sunset Ministry | 501(c)(3) | 2007 | | | |
| Tabernaculo Biblico Bautista El Redentor | 501(c)(3) | 2013 | | | |
| Tabernaculo Biblico de Adoracion | 501(c)(3) | 2007 | | | |
| Tallow Church Fund USA | 501(c)(3) | 2025 | | | |
| Temple of Good Fortune and Wisdom | 501(c)(3) | 2006 | | | |
| Temple of Kun Fusion | 501(c)(3) | 2002 | | | |
| Temple of Shakti | 501(c)(3) | 1996 | | | |
| Temple of the Third Place Inc | 501(c)(3) | 2025 | | | |
| Tendo Institute of U S A | 501(c)(3) | 1999 | | | |
| The Greek Orthodox Church of the Holy Trinity | 501(c)(3) | 2022 | | | |
| The Home of Christ Church in San Francisco | 501(c)(3) | 2001 | | | |
| The Islamic Bulletin Inc | 501(c)(3) | 2020 | $0 | $0 | 2025-12 |
| The Table | 501(c)(3) | 1982 | | | |
| Tibetan Buddhism Association of America | 501(c)(3) | 2003 | | | |
| Trinity San Francisco Opportunity Center Inc | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| True Hope Evangelical Ministry | 501(c)(3) | 2023 | | | |
| Tse Family Association of San Francisco | 501(c)(3) | 2015 | | | |
| Tze Zhan Monastery | 501(c)(3) | 1997 | | | |
| U Dream Center Inc | 501(c)(3) | 2017 | $0 | $0 | 2024-12 |
| United Greek Orthodox Community of San Francisco | 501(c)(3) | 2022 | | | |
| United Peace Foundation | 501(c)(3) | 2001 | | | |
| United Religions Initiative in North America | 501(c)(3) | 2010 | $0 | $0 | 2025-12 |
| United Schneersons Synagogues Inc | 501(c)(3) | 2004 | | | |
| Unity San Francisco | 501(c)(3) | 1970 | | | |
| Universal Awareness Fellowship Inc | 501(c)(3) | 2025 | | | |
| Upper Room | 501(c)(3) | 2025 | $0 | $0 | 2025-06 |
| Varghese Ministries Inc | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Victory Outreach San Francisco South | 501(c)(3) | 2005 | | | |
| Voice of Christ Full Gospel Church | 501(c)(3) | 2008 | | | |
| We Are Church | 501(c)(3) | 2013 | | | |
| Welcome Ministry | 501(c)(3) | 2002 | $0 | $0 | 2025-12 |
| Well Ministries International Inc | 501(c)(3) | 2013 | | | |
| Western American Diocese of Russian Orthodox Church Outside of Russi | 501(c)(3) | 2013 | | | |
| Westside Church of Christ San Francisco Ca | 501(c)(3) | 2004 | | | |
| Wholehearted Sports | 501(c)(3) | 2025 | | | |
| Wisdom Sun | 501(c)(3) | 2013 | | | |
| Without Wall International Ministries | 501(c)(3) | 2016 | | | |
| Yoga Time Inc | 501(c)(3) | 2025 | | | |
| Youth With A Mission-San Francisco | 501(c)(3) | 1995 | | | |
| Zion Mission Korean Baptist Church | 501(c)(3) | 1997 | | | |