| Burnham Ministries International | 501(c)(3) | 1965 | $1.1 million | $5.7 million | 2025-12 |
| Hope International Ministries | 501(c)(3) | 2003 | $1.1 million | $2 million | 2024-12 |
| Islamic Center of Southwest Florida Inc | 501(c)(3) | 2012 | $832,287 | $3.2 million | 2025-12 |
| Harvest Field Church Mii Inc | 501(c)(3) | 2014 | $791,472 | $1.1 million | 2024-12 |
| The Vine Hebron Inc | 501(c)(3) | 2015 | $756,777 | $3.5 million | 2025-12 |
| Hindu Temple of Southwest Florida Inc | 501(c)(3) | 2004 | $622,254 | $3.6 million | 2024-12 |
| St Martin de Porres Outreach Community Ministries Inc | 501(c)(3) | 2014 | $453,254 | $1.3 million | 2025-12 |
| One Way Out Ministries Inc | 501(c)(3) | 2012 | $407,112 | $75,852 | 2023-12 |
| Into the Jordan Ministries Inc | 501(c)(3) | 2014 | $291,742 | $395,199 | 2025-12 |
| Asha Mission Society Inc | 501(c)(3) | 2008 | $280,150 | $673,829 | 2024-12 |
| Southwest Florida Community Prayer Breakfast Inc | 501(c)(3) | 2022 | $207,250 | $198,713 | 2025-12 |
| Ministerio Nuevo Pacto Inc | 501(c)(3) | 2017 | $182,000 | $236,407 | 2022-12 |
| Phuoc Hoa Buddhist Center Inc | 501(c)(3) | 2013 | $162,048 | $4,997 | 2023-12 |
| Lead Global World Ministries Inc | 501(c)(3) | 2022 | $129,476 | $51,200 | 2024-12 |
| Rooted for Life Church Inc | 501(c)(3) | 2018 | $121,668 | $1.2 million | 2025-12 |
| Five Star Christian Ministries | 501(c)(3) | 2020 | $111,728 | $114,562 | 2025-12 |
| USA Chaplain Corp Ministry Inc | 501(c)(3) | 2024 | $94,322 | $1 | 2024-12 |
| Ministerio Internacional Dios Es Fiel Inc | 501(c)(3) | 2014 | $88,485 | $98,308 | 2020-12 |
| Church of God Pentacostas Way of Florida Inc | 501(c)(3) | 1979 | $82,426 | $500,383 | 2025-12 |
| I Planted A Seed Inc | 501(c)(3) | 2008 | $82,406 | $206 | 2025-12 |
| Fort Myers Monthly Meeting of the Religious Society of Friends | 501(c)(3) | 2025 | $63,626 | $899,034 | 2025-12 |
| Evangelical Mission of the Good Sam Aritain Inc | 501(c)(3) | 2026 | $58,416 | $54,736 | 2025-12 |
| Life Lee Interfaith for Empowerment Corp | 501(c)(3) | 2013 | $53,496 | $64,504 | 2025-12 |
| Larry D Ford Ministries Inc | 501(c)(3) | 1998 | $23,191 | $39,170 | 2024-12 |
| The Seek Movement Inc | 501(c)(3) | 2026 | $868 | $505 | 2025-12 |
| 423praise Inc | 501(c)(3) | 2022 | | $509 | 2024-12 |
| Ad Bethel Church Inc | 501(c)(3) | 2005 | | | |
| Amins Academy of Ministries and Services Inc | 501(c)(3) | 2009 | | | |
| Anointed Word Deliverance Center Inc | 501(c)(3) | 1998 | | | |
| Anthony A Spero Ministries Inc | 501(c)(3) | 2007 | $0 | $0 | 2024-12 |
| Antioch Missionary Baptist Church Incorporated of Fort Myers | 501(c)(3) | 2012 | $0 | $0 | 2025-12 |
| Arise Ministries Church Inc | 501(c)(3) | 2022 | | | |
| Assembly of the Firstborn Ministries Inc | 501(c)(3) | 2005 | | | |
| Avalon Druid Order Inc | 501(c)(3) | 2006 | | | |
| Baptist Church Restore Inc | 501(c)(3) | 2014 | | | |
| Bethel Bible Fellowship Church | 501(c)(3) | 2014 | | | |
| Blood Bought Church of God Inc | 501(c)(3) | 2006 | | | |
| Buckingham Community Church Inc | 501(c)(3) | 2015 | | | |
| Center for Islam and Cultural Awareness Inc | 501(c)(3) | 2003 | | | |
| Centro Familiar Cristiano Casa de Adoracion Inc | 501(c)(3) | 2014 | | | |
| Chabad Israeli Center of Fort Myers Inc | 501(c)(3) | 2026 | | | |
| Chabad at Fgcu Inc | 501(c)(3) | 2020 | | | |
| Chavurat Shalom of Southwest Florida Inc | 501(c)(3) | 2024 | $0 | $0 | 2025-12 |
| Church Five Solae Inc | 501(c)(3) | 2024 | | | |
| Church of God By Faith Ministries | 501(c)(3) | 2014 | $0 | $0 | 2021-12 |
| Cielos Abierto Alcanzando Las Almas Inc | 501(c)(3) | 2025 | | | |
| Cornerstone Church of Fort Myers Inc | 501(c)(3) | 2023 | | | |
| Crosses for Kids Corp | 501(c)(3) | 2026 | $0 | $0 | 2025-12 |
| Crossover Ministries Incorporated of SW Florida | 501(c)(3) | 2018 | $0 | $0 | 2025-12 |
| Disciples of the Vine Church Inc | 501(c)(3) | 2026 | | | |
| Eglise de Dieu La Foi Chretienne | 501(c)(3) | 2007 | | | |
| El Rio Church FM Inc | 501(c)(3) | 2025 | | | |
| Elevate Ministries of Florida Inc | 501(c)(3) | 2024 | $0 | $0 | 2025-12 |
| Elevation Ministries Inc | 501(c)(3) | 2010 | | | |
| Enduring Hope Ministries Inc | 501(c)(3) | 2010 | $0 | $0 | 2025-12 |
| Equipt Inc | 501(c)(3) | 2016 | | | |
| Evangelical Church of God Bethlehem Inc | 501(c)(3) | 2025 | | | |
| Faith & Ale - Ft Myers Inc | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Faith Community Missionary Church Inc | 501(c)(3) | 1998 | | | |
| Faith Connections Inc | 501(c)(3) | 2021 | $0 | $0 | 2025-12 |
| Faith Covenant Ministries Comunidade Rocha Eterna | 501(c)(3) | 2000 | | | |
| Faith Fellowship Ministries of Fort Myers Inc | 501(c)(3) | 2015 | | | |
| Faith Partners International Inc | 501(c)(3) | 2013 | $0 | $0 | 2025-12 |
| Fellowship Bible Chapel of Lee County Inc | 501(c)(3) | 2014 | | | |
| First Baptist Church Fort Myers Florida Inc | 501(c)(3) | 2015 | | | |
| Followers of Christ Fellowship Ministries Inc | 501(c)(3) | 2013 | | | |
| Fort Myers Christian Center | 501(c)(3) | 2000 | | | |
| Fort Myers Community Church Inc | 501(c)(3) | 2022 | | | |
| Fountain of Grace International Corp | 501(c)(3) | 2016 | $0 | $0 | 2025-12 |
| Freedom House of Prayer Inc | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| Friendship Community Church | 501(c)(3) | 1997 | | | |
| Ft Myers-Naples Church Inc | 501(c)(3) | 2002 | | | |
| Gateway Church of Southwest Florida Inc | 501(c)(3) | 2016 | | | |
| George Jones Ministries Inc | 501(c)(3) | 2002 | | | |
| Global Church Fellowship | 501(c)(3) | 2002 | $0 | $0 | 2025-12 |
| Global Church Fellowship | 501(c)(3) | 2002 | | | |
| Global Impact Ministries of the Apostolic Faith | 501(c)(3) | 2020 | | | |
| Glorious Church of God of Prophecy | 501(c)(3) | 2009 | | | |
| God Will Ministries Inc | 501(c)(3) | 2010 | | | |
| Godmobile Outreach Inc | 501(c)(3) | 2018 | $0 | $0 | 2025-12 |
| Gods Purpose in Action Ministry SWFL Inc | 501(c)(3) | 2010 | | | |
| Good Samaritan Baptist Center of Fort Myers Inc | 501(c)(3) | 2020 | $0 | $0 | 2023-12 |
| Good Shepherd Pentecostal Church Inc | 501(c)(3) | 2024 | $0 | $0 | 2025-12 |
| Grace New Testament Church in His Blood Inc | 501(c)(3) | 2018 | | | |
| Haiti Bible Mission Inc | 501(c)(3) | 2024 | $0 | $0 | 2024-12 |
| Hallelujah Community Church | 501(c)(3) | 2020 | | | |
| Harvest Bible College and Ministries Inc | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Heal-Align-Impart Family Institute Inc | 501(c)(3) | 2023 | | $1 | 2024-12 |
| Helping Hands Ministries of Jesus Christ Inc | 501(c)(3) | 2009 | | | |
| Hoops On Mission Inc | 501(c)(3) | 2016 | $0 | $0 | 2024-12 |
| House of Prayer Apostolic Church of God IV | 501(c)(3) | 2000 | | | |
| Iglesia Bandera de Cristo Inc | 501(c)(3) | 2002 | | | |
| Iglesia Betel Tierra de Avivamiento Corp | 501(c)(3) | 2017 | | | |
| Iglesia Cristiana Nueva Jerusalem I NC | 501(c)(3) | 2026 | | | |
| Iglesia Cristiana Resplandece Inc | 501(c)(3) | 2000 | | | |
| Iglesia Monte de Jehova Inc | 501(c)(3) | 2012 | | | |
| Iglesia Pent Puerta Del Cielo | 501(c)(3) | 2020 | | | |
| Igreja Assembleia de Deus Ministerio Agape Inc | 501(c)(3) | 2017 | | | |
| Interfaith Action Group of Southwest Florida Inc | 501(c)(3) | 2018 | $0 | $0 | 2025-12 |
| Jerusalem Missionary Baptist Church Inc | 501(c)(3) | 2010 | | | |
| Kingdom Warriors Taking the City | 501(c)(3) | 2022 | $0 | $0 | 2025-12 |
| Living Hope Counseling of Southwest Florida Inc | 501(c)(3) | 2017 | $0 | $0 | 2025-12 |
| Lo-Debar Community Church | 501(c)(3) | 2019 | | | |
| Masters Pasture Ministries | 501(c)(3) | 2009 | | | |
| Ministerio Jehova Jireh Inc | 501(c)(3) | 2026 | | | |
| Ministerio Jesucristo Trompeta de Dios | 501(c)(3) | 2013 | | | |
| Ministerio Oasis En Jesus Inc | 501(c)(3) | 2009 | | | |
| Ministerio Un Paso de Fe | 501(c)(3) | 1964 | | | |
| Ministerio de Jesucristo Revelacion Y Fuego Inc | 501(c)(3) | 2023 | | | |
| Mision Vida Cristiana Inc | 501(c)(3) | 2013 | $0 | $6,162 | 2025-12 |
| Mount Zion Missionary Baptist Church | 501(c)(3) | 2001 | | | |
| Mt Sinai Baptist Church Inc | 501(c)(3) | 2004 | $0 | $0 | 2025-12 |
| New Fire Discipleship | 501(c)(3) | 2026 | | | |
| New Hope Presbyterian Church | 501(c)(3) | 1982 | | | 2011-12 |
| New Life Hope Ministries | 501(c)(3) | 2010 | | | |
| Next Level Church Inc | 501(c)(3) | 2002 | | | |
| One More Home Inc | 501(c)(3) | 2021 | $0 | $0 | 2024-12 |
| Paul Lodato Ministries Inc | 501(c)(3) | 2018 | $0 | $0 | 2025-12 |
| Pierre Metellus Faith Evangelistic Ministries Fem | 501(c)(3) | 2008 | | | |
| Pinami Cares Trust Inc | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Propagators of the Gospel Inc | 501(c)(3) | 2024 | $0 | $0 | 2025-12 |
| Purpose and Legacy Center | 501(c)(3) | 2025 | | | |
| Reach More Ministries | 501(c)(3) | 2022 | $0 | $0 | 2023-12 |
| Refuge Church FM Corp | 501(c)(3) | 2017 | | | |
| Remnant Gathering Inc | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Renaissance Ministries of Dwain Upton Inc | 501(c)(3) | 1998 | $0 | $0 | 2025-12 |
| Ride Nature Corporation | 501(c)(3) | 2019 | | | |
| Root Bible | 501(c)(3) | 2020 | $0 | $0 | 2025-12 |
| Safe Harbor Ministries Inc | 501(c)(3) | 1996 | | | |
| Saint Nicholas Orthodox Monastery Corp | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| Saint Raphael S By the Sea Corporation | 501(c)(3) | 2010 | | | |
| Samudrabadra Kadampa Buddhist Center | 501(c)(3) | 2010 | | | |
| San Carlos Worship Center Inc | 501(c)(3) | 2007 | | | |
| Second Church Assembly of God | 501(c)(3) | 2006 | | | |
| Second Haitian Baptist Church Offort Myers Inc | 501(c)(3) | 2007 | | | |
| See His Face Outreach Center Inc | 501(c)(3) | 2024 | | | |
| Shalom Life Center Inc | 501(c)(3) | 2016 | | | |
| Simply Simple Worship Inc | 501(c)(3) | 2016 | $0 | $0 | 2025-12 |
| Soul Seed Ministries | 501(c)(3) | 2018 | | | |
| South Side Church of Christ Inc | 501(c)(3) | 2023 | | | |
| Speak To the Mountain Inc | 501(c)(3) | 2024 | $0 | $0 | 2025-12 |
| St Marys Indian Orthodox Congregation of Southwest Florida | 501(c)(3) | 2020 | | | |
| Summit Church Inc | 501(c)(3) | 2004 | | | |
| The Community Free Synagogue | 501(c)(3) | 2007 | | | |
| Thomas A Edison Congregational Church | 501(c)(3) | 2012 | | | |
| Thomas Felber Inc | 501(c)(3) | 2022 | $0 | $0 | 2023-12 |
| Touched By the Master Ministries | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| Transformation Church of Fort Myers | 501(c)(3) | 2024 | | | |
| Trinity Christian Outreach Ministeries | 501(c)(3) | 2017 | | | |
| Triumph Ministry Inc | 501(c)(3) | 2024 | | | |
| Villas Grace Inc | 501(c)(3) | 2019 | | | |
| Walter Gimenez Ministries Inc | 501(c)(3) | 2013 | $0 | $0 | 2025-12 |
| Well Gulf Coast Inc | 501(c)(3) | 2017 | | | |
| Word of Life Ministries | 501(c)(3) | 1997 | | | |
| Wow Worship Center Inc | 501(c)(3) | 2024 | $0 | $0 | 2025-12 |