| Metanoia Inc | 501(c)(3) | 2025 | $8 million | $7.9 million | 2024-12 |
| Hillel the Foundation for Jewish Campus Life | 501(c)(3) | 1993 | $5.7 million | $53.7 million | 2025-06 |
| RBN Foundation | 501(c)(3) | 2023 | $2.7 million | $907,352 | 2024-12 |
| Rivendell Institute Inc | 501(c)(3) | 2001 | $917,637 | $1.8 million | 2024-12 |
| Center for Early African Christianity Inc | 501(c)(3) | 2008 | $486,166 | $1 million | 2024-12 |
| Chapel Haven Endowment Inc | 501(c)(3) | 2008 | $410,217 | $14.9 million | 2025-06 |
| Shabtai | 501(c)(3) | 2020 | $328,126 | $1.5 million | 2024-12 |
| Daughters of Isabella | 501(c)(8) | 1947 | $310,052 | $935,144 | 2026-04 |
| Holy Hill Church of God International Ministry Inc | 501(c)(3) | 2022 | $147,205 | $1.9 million | 2024-12 |
| Religious Education Association Inc | 501(c)(3) | 2018 | $135,415 | $490,303 | 2025-12 |
| Jubilee New Haven Inc | 501(c)(3) | 2019 | $109,313 | $360,503 | 2025-12 |
| New Haven Mikvah Inc | 501(c)(3) | 2024 | $94,664 | $169,942 | 2025-12 |
| Charismatic Renewal Ministries Praise Center | 501(c)(3) | 2011 | $82,443 | $122,969 | 2022-12 |
| Alma Radio Inc | 501(c)(3) | 2021 | $69,250 | $64,592 | 2024-12 |
| 300 Shul | 501(c)(3) | 2025 | | | |
| A Secret Garden | 501(c)(3) | 2007 | | | |
| African Christian Biography Friends Corporation | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| All Nations Christian Church | 501(c)(3) | 2013 | | | |
| Anointed Action Ministeries Inc | 501(c)(3) | 1998 | | | |
| Anointed Tabernacle Ministries Inc | 501(c)(3) | 1999 | | | |
| Asociacion Ministerial Evangelica Hispana de New Haven | 501(c)(3) | 2009 | | | |
| Basileia Outreach Ministry | 501(c)(3) | 2016 | | | |
| Beis Moshiach Inc | 501(c)(3) | 2025 | | | |
| Beth Hamedrosh Hago Dol Binai | 501(c)(3) | 2025 | | | |
| Beulah Heights Church | 501(c)(3) | 2003 | | | |
| Breaking Chains Ministries Cathedral of Miracles Inc | 501(c)(3) | 2025 | | | |
| Casa de Oracion Y Adoracion | 501(c)(3) | 2024 | | | |
| Cathedral of Higher Praise Church of God of Prophecy Inc | 501(c)(3) | 2002 | | | |
| Chabad at Yale University Inc | 501(c)(3) | 2015 | | | |
| Chabad of Barrington Inc | 501(c)(3) | 2008 | | | |
| Chabad of Downtown New Haven Inc | 501(c)(3) | 2020 | | | |
| Chabad of Westville Inc | 501(c)(3) | 2020 | | | |
| Children of the Wilderness Outreach Ministry | 501(c)(3) | 2011 | $0 | $0 | 2024-12 |
| Christian Love Center Church Incorporated | 501(c)(3) | 1996 | | | |
| Church On the Rock Global Ministrie S Inc | 501(c)(3) | 2026 | | | |
| Church of Christ Deliverance Temple of God Inc | 501(c)(3) | 2000 | | | |
| Church of New Beginnings | 501(c)(3) | 2002 | | | |
| Church of the Ascent Inc | 501(c)(3) | 2025 | | | |
| Churches of Christ in Prayer Inc | 501(c)(3) | 2006 | | | |
| Congregacion de Yahweh Nuestro Elohim | 501(c)(3) | 2006 | | | |
| Congregation BH Inc | 501(c)(3) | 2019 | | $9.3 million | 2024-12 |
| Congregation Beth El-Keser Israel | 501(c)(3) | 2000 | | | |
| Congregation Chabad Lubavitch of New Haven Inc | 501(c)(3) | 2015 | | | |
| Covenant Community Church Corporation | 501(c)(3) | 2003 | | | |
| Danials Den Inc | 501(c)(3) | 2006 | | | |
| Daylight Saving Ministries | 501(c)(3) | 2005 | | | |
| Deeper Life Bible Church - New Haven District | 501(c)(3) | 2022 | | | |
| El Bethel the New England House of Prayer Inc | 501(c)(3) | 2019 | | | |
| El Fundamento de La Fe Inc | 501(c)(3) | 2017 | | | |
| Elm City Vineyard Church | 501(c)(3) | 2009 | | | |
| Ephesians 6 Project Inc | 501(c)(3) | 2022 | $0 | $0 | 2025-12 |
| Every Need Church Inc | 501(c)(3) | 2021 | | | |
| Faith Power and Deliverance Center Inc | 501(c)(3) | 2007 | | | |
| Faith Revolution Church | 501(c)(3) | 2020 | | | |
| Faith Temple Deliverance Center Inc | 501(c)(3) | 2013 | | | |
| First Calvary Baptist Church | 501(c)(3) | 1998 | | | |
| Flock of God Ministries Inc | 501(c)(3) | 2007 | | | |
| Free Will Ministry of Jesus Christ Inc | 501(c)(3) | 1996 | | | |
| Freewill Holiness Churches Inc | 501(c)(3) | 1998 | | | |
| Friendship Circle South Jerusalem Inc | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Friendship Missionary Baptist Church of New Haven Inc | 501(c)(3) | 1999 | | | |
| Fundacion Juntos Construiremos | 501(c)(3) | 2022 | $0 | $0 | 2023-12 |
| Gods Corner Church Inc | 501(c)(3) | 1997 | | | |
| Gods House - Church of Worship | 501(c)(3) | 2015 | | | |
| Gods House Ministries | 501(c)(3) | 2002 | | | |
| Grace and Peace Catheral International Inc | 501(c)(3) | 2016 | | | |
| Greater Assembly of Judah International Corp | 501(c)(3) | 2024 | | | |
| Greater New Haven Clergy Association Inc | 501(c)(3) | 2018 | $0 | $0 | 2024-12 |
| Green & Sklarz Foundation Trust | 501(c)(3) | 2015 | | $14,768 | 2025-12 |
| Healing and Deliverance Outreach Ministries Incorporation | 501(c)(3) | 2016 | | | |
| Heart To Heart Community Outreach Church Inc | 501(c)(3) | 2022 | | | |
| His Divine Will Fellowship | 501(c)(3) | 2024 | | | |
| Holy Hill Churches World Wide Inc | 501(c)(3) | 1997 | | | |
| House of Prayer for All People Inc | 501(c)(3) | 2026 | | | |
| Iglesia Cristiana Bet-El | 501(c)(3) | 2023 | | | |
| Iglesia Cristiana Manantial de Aguas Vivas | 501(c)(3) | 2015 | | | |
| Iglesia Cristiana Multicultural Un Paso de Fe | 501(c)(3) | 2026 | | | |
| Iglesia Cristiana de Compasion La Nueva Generacion | 501(c)(3) | 2013 | | | |
| Iglesia Dios Admirable | 501(c)(3) | 2013 | | | |
| Iglesia El Sermon Del Monte Inc | 501(c)(3) | 2007 | | | |
| Iglesia Evangelica Bethel Casa de Dios Puerta Del Cielo | 501(c)(3) | 2022 | | | |
| Iglesia Pentecostal Dios Es Fiel LLC | 501(c)(3) | 2021 | | | |
| Iglesia Pentecostal Lumbrera de Dios Inc | 501(c)(3) | 2010 | $0 | $1 | 2024-12 |
| Iglesia Pentecostal Unida Hispana Inc El Gran Yo Soy New Haven CT | 501(c)(3) | 2018 | $0 | $0 | 2025-12 |
| Iglesia Rios de Agua Viva | 501(c)(3) | 2014 | | | |
| Iglesia de Dios Casa de Restauracion Corp | 501(c)(3) | 2026 | | | |
| Immanuel Baptist Church Inc | 501(c)(3) | 1998 | | | |
| Indigo Blue Inc | 501(c)(3) | 2004 | | | |
| Jehova Es Mi Pastor Inc | 501(c)(3) | 2024 | | | |
| Jehovah Rapha Healing Ministries | 501(c)(3) | 2022 | $0 | $0 | 2024-12 |
| Jesus Stands for Love and Justice Ministries | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| Jewish Israeli Center New Haven Inc | 501(c)(3) | 2024 | | | |
| Kollol Tifereth Zkeinim Levi Yitzchak Vchocmas Noshim Inc | 501(c)(3) | 2014 | | | |
| Liberacion New Haven Mundial Inc | 501(c)(3) | 2023 | | | |
| Life Kingdom Outreach Ministries Inc | 501(c)(3) | 2022 | | | |
| Lord Center Inc | 501(c)(3) | 2022 | | | |
| Mentors Table Ministries Inc | 501(c)(3) | 2024 | $0 | $0 | 2025-12 |
| Ministry of Helps Foundation Inc | 501(c)(3) | 1999 | | | |
| Miracle Temple Church of God | 501(c)(3) | 2004 | | | |
| Mitzvah Tank USA Inc | 501(c)(3) | 2025 | | | |
| Morning Glory Pentecostal | 501(c)(3) | 2005 | | | |
| Mount Hope Temple Inc | 501(c)(3) | 1997 | | | |
| Mt Zion Temple Pentecostal | 501(c)(3) | 2006 | | | |
| Muslim Endorsement Council Inc | 501(c)(3) | 2013 | $0 | $0 | 2025-12 |
| Nawiskill | 501(c)(3) | 2026 | $0 | $0 | 2026-03 |
| Nehemiahs Day Outreach Ministries | 501(c)(3) | 2015 | | | |
| New Birth Church of Christ | 501(c)(3) | 2011 | | | |
| New Freedom Missionary Baptist Church Inc | 501(c)(3) | 1998 | | | |
| New Haven Chevrah Kadisha Inc | 501(c)(3) | 2024 | | | |
| New Lighthouse Ministries Inc | 501(c)(3) | 2000 | | | |
| New Vision Ministry | 501(c)(3) | 2009 | | | |
| Next Level Ministries Church | 501(c)(3) | 2009 | | | |
| Now Faith Is Ministries Inc | 501(c)(3) | 2019 | $0 | $0 | 2023-12 |
| Now Faith Ministries | 501(c)(3) | 2015 | $0 | $0 | 2025-12 |
| Ohel Yosef Yitzchok Inc | 501(c)(3) | 2017 | $0 | $0 | 2025-12 |
| Peniel Community Church | 501(c)(3) | 2014 | | | |
| Pentecostal Church Door of Salvation Inc | 501(c)(3) | 2000 | | | |
| Power House Temple of Deliverance Inc | 501(c)(3) | 2006 | | | |
| Presbyterian Promise Inc | 501(c)(3) | 2001 | $0 | $0 | 2025-12 |
| Primera Iglesia Pentecostes Jesucri Sto Vive Inc | 501(c)(3) | 2026 | | | |
| Pure United Holiness Church | 501(c)(3) | 2005 | | | |
| Radio Amor Inc | 501(c)(3) | 2023 | $0 | $0 | 2023-12 |
| Red Apostolica Com Crist de Rest A Las Nac Internacional | 501(c)(3) | 2017 | | | |
| Rehoboth Sanctified Church of Our Lord and Saviour Jesus Christ Inc | 501(c)(3) | 2001 | | | |
| Rim City Church Connecticut Inc | 501(c)(3) | 2023 | | | |
| Rising Hope Ministries International Incorporated | 501(c)(3) | 2022 | $0 | $0 | 2025-12 |
| Rock Tabernacle Ministries | 501(c)(3) | 2002 | | | |
| Salvation and Deliverance Church CT Inc | 501(c)(3) | 2023 | $0 | $0 | 2023-12 |
| Shiloh Missionary Baptist Church | 501(c)(3) | 2003 | | | |
| Solomon House at Yale | 501(c)(3) | 2026 | | | |
| Somos Una Familia Inc | 501(c)(3) | 2023 | $0 | $0 | 2025-12 |
| Springs of Life-Giving Water Church Inc | 501(c)(3) | 2007 | | | |
| St Joseph of Arimathea Church | 501(c)(3) | 2014 | | | |
| St Matthew Ufw Baptist Church | 501(c)(3) | 1997 | | | 2024-12 |
| St Paul Union American Methodist Episcopal Church | 501(c)(3) | 2001 | | | |
| St Stephens Holiness Church Christ Deliverance Center Inc | 501(c)(3) | 2000 | | | |
| Tabernacle of Faith and Deliverance Ministries Inc | 501(c)(3) | 2024 | | | |
| Temple of Deliverance Church Connecticut Inc | 501(c)(3) | 1999 | | | |
| The 180 Center Corp | 501(c)(3) | 2016 | | | |
| Thomas Chapel Church of Christ Disciples | 501(c)(3) | 2002 | | | |
| True Worship Church Inc | 501(c)(3) | 2001 | | | |
| Una Iglesia Para La Ciudad | 501(c)(3) | 2020 | | | |
| Upon This Rock Ministries Inc | 501(c)(3) | 2009 | | | |
| Upright Ministries | 501(c)(3) | 2018 | $0 | $0 | 2025-12 |
| Varick Memorial A M E Zion Church | 501(c)(3) | 2014 | | | 2025-05 |
| Victory Temple Church Inc | 501(c)(3) | 2001 | | | |
| WLM Ministries Inc | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| Walk of Faith Church of Christ Deciples of Christ | 501(c)(3) | 2010 | | | |
| Way of the Cross Bible Way Church Inc | 501(c)(3) | 2014 | | | |
| Yaweh Cathedral International Ministries Inc | 501(c)(3) | 2014 | | | |