| Columbia College | 501(c)(3) | 1943 | $69.1 million | $233.9 million | 2025-06 |
| Stephens College | 501(c)(3) | 1944 | $32.5 million | $94 million | 2025-06 |
| Deaflead | 501(c)(3) | 1995 | $18.3 million | $6.2 million | 2025-06 |
| Mobius | 501(c)(3) | 2010 | $10.4 million | $4.1 million | 2025-06 |
| Columbia Independent School Inc | 501(c)(3) | 1997 | $7.4 million | $26 million | 2025-06 |
| University of Missouri Alumni Association | 501(c)(3) | 1946 | $3.2 million | $19.5 million | 2025-06 |
| Veterinary Cancer Society | 501(c)(3) | 2004 | $1.6 million | $4 million | 2025-12 |
| Missourian Publishing Association Inc | 501(c)(3) | 1927 | $1.4 million | $159,948 | 2025-06 |
| Columbia Montessori Society Inc | 501(c)(3) | 1968 | $1.1 million | $362,507 | 2025-08 |
| Mary Lee Johnston Community Learning Center | 501(c)(3) | 1955 | $1 million | $459,052 | 2025-12 |
| Christian Campus House Inc | 501(c)(3) | 1969 | $1 million | $2 million | 2025-06 |
| Sigma Nu Fraternity | 501(c)(7) | 1940 | $980,024 | $105,050 | 2025-06 |
| Alpha Tau Omega-Gamma Rho Housing Corporation | 501(c)(7) | 2006 | $934,140 | $572,907 | 2025-06 |
| Childrens House of Columbia Inc | 501(c)(3) | 1972 | $781,168 | $415,939 | 2025-05 |
| First Chance for Children | 501(c)(3) | 2003 | $714,091 | $139,911 | 2024-12 |
| La Petite Ecole | 501(c)(3) | 2006 | $653,177 | $487,421 | 2025-07 |
| Windsor Street Montessori School | 501(c)(3) | 2014 | $634,850 | $512,261 | 2026-05 |
| Islamic School of Columbia Missouri | 501(c)(3) | 2014 | $429,716 | $162,397 | 2025-12 |
| Nora Stewart Early Learning Center | 501(c)(3) | 1948 | $383,416 | $246,042 | 2024-12 |
| University of Missouri Medical School Foundation Incorporated | 501(c)(3) | 1959 | $346,837 | $5.5 million | 2025-03 |
| Noor Academy Incorporated | 501(c)(3) | 2024 | $321,272 | $10,617 | 2024-12 |
| Zeta Phi Society-Foundation | 501(c)(3) | 1990 | $306,934 | $3.8 million | 2024-12 |
| Foundation of the Missouri United Methodist Church Columbia | 501(c)(3) | 2016 | $261,706 | $7.1 million | 2024-12 |
| Sigma Phi Epsilon Fraternity Inc | 501(c)(7) | 1941 | $233,045 | $6,779 | 2025-06 |
| Columbia Public School District Foundation | 501(c)(3) | 1996 | $202,147 | $2.8 million | 2025-12 |
| Columbia Christian Academy | 501(c)(3) | 2018 | $198,666 | $64,697 | 2024-06 |
| Most Policy Initiative | 501(c)(3) | 2020 | $133,592 | $381,297 | 2025-06 |
| Columbia Stem Alliance Foundation | 501(c)(3) | 2018 | $114,281 | $98,278 | 2025-12 |
| Ess Foundation | 501(c)(3) | 2019 | $111,302 | $131,220 | 2024-12 |
| Wakonse Foundation | 501(c)(3) | 2004 | $106,063 | $118,616 | 2025-12 |
| University of Missouri College of Engineering Foundation | 501(c)(3) | 2010 | $105,337 | $219,125 | 2024-12 |
| Friends of the Public Library Inc | 501(c)(3) | 2002 | $101,614 | $52,406 | 2025-12 |
| Show-Me School-Based Alliance of Missouri | 501(c)(3) | 2023 | $100,000 | $137,184 | 2025-06 |
| Humpty Dumpty Christian Co-Op Preschool Inc | 501(c)(3) | 1968 | $76,618 | $18,853 | 2025-06 |
| University of Missouri Columbia Student Bar Association | 501(c)(3) | 2013 | $75,532 | $36,551 | 2026-05 |
| Columbia Educational Robotics Foundation | 501(c)(3) | 2015 | $69,279 | $60,638 | 2025-12 |
| Christina Bohn Foundation | 501(c)(3) | 2024 | $52,609 | $13,452 | 2025-12 |
| Rock Bridge High School Show Choir Boosters | 501(c)(3) | 2009 | $52,364 | $55,948 | 2024-12 |
| Hickman Athletic Booster Club | 501(c)(3) | 2021 | $44,286 | $49,327 | 2025-06 |
| American Board of Professional Psychology Foundation | 501(c)(3) | 2010 | $41,217 | $315,399 | 2025-12 |
| Evergreen Project | 501(c)(3) | 2020 | $40,045 | $139,920 | 2024-12 |
| Centro Latino de Salud Educacion Y Cultura | 501(c)(3) | 2000 | $31,829 | $185,834 | 2025-12 |
| Rho Chapter Sigma Nu Educational Foundation | 501(c)(3) | 2015 | $28,566 | $579 | 2025-12 |
| Missouri Veterinary Educational Service | 501(c)(3) | 1983 | $17,084 | $97,333 | 2025-06 |
| University of Missouri Orthopaedicassociationdept of Orth | 501(c)(3) | 2012 | $7,560 | $64,076 | 2024-12 |
| College of Veterinary Medicine Clas S of 2029 | 501(c)(7) | 2026 | $1,700 | $1,700 | 2025-12 |
| Acbsp Region 8 | 501(c)(3) | 2018 | $0 | $0 | 2026-02 |
| Acharya Initiatives Inc | 501(c)(3) | 2026 | | | |
| Ai for Everyone Academy | 501(c)(3) | 2026 | $0 | $0 | 2025-12 |
| Alpha Hart Lewis Pta | 501(c)(3) | 1971 | $0 | $0 | 2026-06 |
| Alpha Sigma Phi Fraternity Inc | 501(c)(7) | 1941 | $0 | $0 | 2024-06 |
| Ambleside School of Columbia | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| American Association of University Women Inc | 501(c)(4) | 2010 | $0 | $0 | 2026-06 |
| Arnell L Monroe Scholarship Foundation | 501(c)(3) | 2026 | | | |
| Bruin Band Boosters | 501(c)(3) | 2007 | $0 | $0 | 2025-05 |
| Business Entrepreneurship & Tax Law Review | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| Cale Impact Foundation | 501(c)(3) | 2025 | $0 | $0 | 2026-06 |
| Cedar Ridge Family Teacher Organization | 501(c)(3) | 2017 | $0 | $0 | 2023-12 |
| Center for Psychosocial Organization Studies | 501(c)(3) | 2022 | $0 | $0 | 2025-06 |
| Central Missouri Radio Association | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Central Missouri Sigma Chi Alumni | 501(c)(10) | 2005 | $0 | $0 | 2025-12 |
| College of Engineering Graduate Student Association | 501(c)(3) | 2025 | | | |
| Columbia African American Association Memorial Scholarship F | 501(c)(3) | 2012 | $0 | $0 | 2025-12 |
| Columbia Quarterback Club | 501(c)(3) | 2011 | $0 | $10,608 | 2024-12 |
| Delta Xi of Delta Delta Delta Educational Foundation | 501(c)(3) | 1998 | $0 | $0 | 2026-05 |
| Donald Howard Scholarship Fund | 501(c)(3) | 2006 | $0 | $0 | 2024-12 |
| Educational Foundation of the Alpha Kappa Chapter of the Kappa Alpha | 501(c)(3) | 2016 | $0 | $0 | 2024-06 |
| English for All | 501(c)(3) | 2025 | $0 | $0 | 2024-12 |
| Escuelita Alegria | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Fill Youth School in Columbia | 501(c)(3) | 2022 | $0 | $0 | 2023-07 |
| Freeair Literacy Foundation | 501(c)(3) | 2023 | $0 | $0 | 2025-12 |
| Friends of the Atelier | 501(c)(3) | 2023 | $0 | $0 | 2025-12 |
| Hallsville Youth Development Foundation | 501(c)(3) | 2011 | $0 | $0 | 2025-12 |
| Hickman Cheer and Dance Boosters | 501(c)(3) | 2022 | $0 | $0 | 2025-12 |
| Homeschool Enrichment and Teaching | 501(c)(3) | 2018 | $0 | $0 | 2025-12 |
| Infopower International | 501(c)(3) | 2015 | $0 | $0 | 2024-12 |
| International Conference On Pig Reproduction | 501(c)(3) | 1995 | $0 | $0 | 2024-12 |
| International Society of Weekly Newspaper Editors Foundation Inc | 501(c)(3) | 2003 | $0 | $0 | 2025-12 |
| Jack E Dawson Scholarship Fund | 501(c)(3) | 2009 | | $384,607 | 2025-12 |
| Japanese Student Association at University of Missouri | 501(c)(3) | 2023 | $0 | $0 | 2024-12 |
| Keeping Missouri Roads Safe | 501(c)(3) | 2026 | | | |
| Koller Educational Foundation | 501(c)(3) | 2011 | | $61,418 | 2025-06 |
| Landlocked Opera Inc | 501(c)(3) | 2019 | $0 | $0 | 2026-06 |
| League of Women Voters Columbia Boone County Education Fund | 501(c)(3) | 2025 | $0 | $0 | 2025-06 |
| Little Sisters of the Gold Rose | 501(c)(3) | 2026 | $0 | $0 | 2025-12 |
| Locust Street Expressive Arts Elementary | 501(c)(3) | 2025 | $0 | $0 | 2025-06 |
| Master of Health Administration Graduate Student Association | 501(c)(3) | 2025 | | | |
| McGivney Catholic Education Fund Inc | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| Minority Mens Network Educational Foundation | 501(c)(3) | 2002 | $0 | $0 | 2025-05 |
| Missouri Artisans Association | 501(c)(3) | 2003 | $0 | $0 | 2025-06 |
| Missouri Association of Code Enforcement | 501(c)(3) | 2015 | $0 | $0 | 2025-12 |
| Missouri Lodge of Research Foundation | 501(c)(3) | 2014 | $0 | $0 | 2025-10 |
| Missouri Nutrition Alliance | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| Missouri Quizbowl Alliance | 501(c)(3) | 2018 | $0 | $0 | 2026-07 |
| Missouri Sunshine Coalition Inc | 501(c)(3) | 2017 | $0 | $0 | 2025-12 |
| Missouri Writing Project Collaborative | 501(c)(3) | 2017 | $0 | $0 | 2025-06 |
| Missouri Youthbuild Coalition | 501(c)(3) | 2024 | | | |
| Mizzou Computing Association | 501(c)(3) | 2024 | $0 | $0 | 2024-05 |
| Mizzou Engineering Student Council | 501(c)(3) | 2023 | $0 | $0 | 2024-11 |
| Mizzou Racing Co | 501(c)(3) | 2024 | $0 | $0 | 2025-08 |
| Mucvm2028 | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Music Teachers National Association Inc | 501(c)(3) | 1999 | $0 | $0 | 2024-12 |
| National Association of Teachers of Singing Inc | 501(c)(3) | 2009 | $0 | $0 | 2025-12 |
| National Black American Law Students Association Inc | 501(c)(3) | 2019 | $0 | $0 | 2025-09 |
| Once An Orphan Always An Orphan Foundation | 501(c)(3) | 2024 | | | |
| Our History We Must Not Forget | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Parent Booster USA Inc | 501(c)(3) | 2005 | $0 | $0 | 2025-07 |
| Pettis County Citizens for Land Protection | 501(c)(3) | 2016 | $0 | $0 | 2025-12 |
| Pta Missouri Congress | 501(c)(3) | 1971 | $0 | $0 | 2026-06 |
| Replenish Development | 501(c)(3) | 2024 | | | |
| Scholarship Success Foundation | 501(c)(3) | 2025 | | | |
| Shelter Insurance Foundation | 501(c)(3) | 1981 | | $19.6 million | 2025-12 |
| Shepard Parent-Teacher-Student Organization | 501(c)(3) | 2016 | $0 | $0 | 2026-07 |
| Sigma Pi Fraternity Intl Gamma Sigm A Chapter | 501(c)(7) | 2026 | | | |
| The Copula Program | 501(c)(3) | 2026 | $0 | $0 | 2026-07 |
| The Golden Key Scholarship Fund Inc | 501(c)(3) | 1985 | | $973,723 | 2025-12 |
| The Hagan Scholarship Foundation | 501(c)(3) | 2008 | | $293.5 million | 2024-12 |
| Timurs Preschool | 501(c)(3) | 2026 | | | |
| Tobacco Free Missouri | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| W R Bynum Medical Arts Institute | 501(c)(3) | 2009 | $0 | $0 | 2025-12 |
| Wild Trek | 501(c)(3) | 2024 | $0 | $0 | 2023-12 |