The 1998 National Congregations Study (Wave I) was supported by a major grant from Lilly Endowment, Inc., and by additional grants from Smith Richardson Foundation, Inc., Louisville Institute, Nonprofit Sector Research Fund of the Aspen Institute, and Henry Luce Foundation, Inc.

The 2006–07 National Congregations Study (Wave II) was also supported by a major grant from the Lilly Endowment, and by additional grants from Kellogg Foundation, National Science Foundation, and Louisville Institute.

The 2012 National Congregations Study (Wave III) was once again supported by a major grant from the Lilly Endowment, and by additional grants from Pew Research Center's Religion and Public Life Project, Louisville Institute, Center for the Study of Religion and American Culture at Indiana University-Purdue University Indianapolis, RAND Corporation, and Church Music Institute. It also received generous support from Duke University and from the National Science Foundation via NSF's support of the General Social Survey.

The 2018-19 National Congregations Study (Wave IV) again was supported by a major grant from the Lilly Endowment, and by a major grant from the John Templeton Foundation. It received additional financial support from the Louisville Institute, Pew Research Center's Forum on Religion & Public Life, and the National Science Foundation via the module competition that subsidized including questions about respondents’ congregations on the 2018 General Social Survey.