Templeton became wealthy as a contrarian investor, and wanted to support progress in religious and spiritual knowledge, especially at the intersection of religion and science.

The foundation administers the annual Templeton Prize for achievements in the field of spirituality, including those at the intersection of science and religion.

It has an extensive grant-funding program (around $150 million per year as of 2016)[7] aimed at supporting research in physics, biology, psychology, and the social sciences as well as philosophy and theology.

[4] More recent winners of the Templeton Prize have included the Dalai Lama in 2012,[19] King Abdullah II of Jordan in 2018,[20] Brazilian Jewish physicist and astronomer Marcelo Gleiser in 2019,[21] and primatologist Jane Goodall in 2021.

[4] While most of its funding goes to topics in science, philosophy, and religion, around 40 percent of its annual grants go to character development, genius, freedom, free enterprise, and fields associated with classical liberalism.

[4] Some research programs supported by the foundation included the development of positive psychology by Martin Seligman, Angela Duckworth and others;[23] the Black Hole Initiative at Harvard University;[24][25] the Gen2Gen Encore Prize; the World Science Festival;[26] Pew religious demographics surveys;[27] and programs that engage with Buddhist, Jewish, Muslim, Hindu, Orthodox, Catholic, and Protestant traditions, including support for dialogue with scientists in synagogues,[28] and a grant for advancing scientific literacy in madrasas.

[35][36][37] Notable principal participants include Sheperd Doeleman, Peter Galison, Avi Loeb, Ramesh Narayan, Andrew Strominger, and Shing-Tung Yau.

A 2014 grant of $4.9 million supports an effort at Arizona State University by paleoanthropologist Donald Johanson to explore how we became human, and a $3.2 million grant to Indiana University and the Stone Age Institute supports the study of "what factors led human ancestors to develop skills like making tools, developing language, and seeking out information".

[45] The funding was used to solve a riddle that had puzzled historians, classicists, linguists, anthropologists and archaeologists for 200 years - whether the bulk of the European civilization had arrived from Anatolia or the Pontic Steppes of Central Asia, and how Indo-European languages spread over an enormous geographical area from Britain to India, becoming the largest linguistic group today.

[46] The funding was used to embrace a multi-disciplinary approach and crowd-sourced results before the final manuscripts were completed, receiving commentary and feedback from academics of various institutions on several continents, according to geneticist David Reich,[46] lead researcher on the project.

[55] Harold G. Koenig, Dale Mathews, David Larson, Jeffrey Levin, Herbert Benson and Michael McCullough are scholars to whom the foundation has provided funds to "report the positive relations" between religion and medicine.

The French National Center for Scientific Research (CNRS) has been critical of the foundation for funding "initiatives to bring science and religion closer together.

In a 2010 article on his Discover magazine blog, Mooney wrote, "I can honestly say that I have found the lectures and presentations that we've heard here to be serious and stimulating.

[71] Wired magazine noted in 1999 that "the scientific-review and grant-award process at the Templeton Foundation is run by Charles Harper, an Oxford-trained planetary scientist specializing in star and planet formation who has a degree in theology.

[74] Richard Dawkins, in his 2006 book The God Delusion, interprets Horgan as saying that "Templeton's money corrupts science", and characterizes the prize as going "usually to a scientist who is prepared to say something nice about religion".

According to him, the foundation supports Christian bias in the field of religious studies, by deliberately imposing constraints to steer the results of the research.

[71] Paul Davies, physicist and 1995 Templeton Prize laureate, gave a defense of the foundation's role in the scientific community in the Times Higher Education Supplement in March 2005.

[79] Harper Jr. told The New York Times the same year: "From the point of view of rigor and intellectual seriousness, the intelligent design people don't come out very well in our world of scientific review".

[80] Some organizations funded by the foundation in the 1990s gave book-writing grants to Guillermo Gonzalez and to William Dembski, proponents of intelligent design who later joined the Discovery Institute.

[4][81] The foundation also gave money directly to the Discovery Institute which in turn passed it through to Baylor University, which used the funds to support Dembski's salary at its short-lived Michael Polanyi Center.

"[4][80] In March 2009, the Discovery Institute accused the foundation of blocking its involvement in Biological Evolution: Facts and Theories, a Vatican-backed, Templeton-funded conference in Rome.

A 1997 article in Slate written by David Plotz said the foundation had given a significant amount of financial support to groups, causes and individuals considered conservative, including gifts to Gertrude Himmelfarb, Milton Friedman, Walter E. Williams, Julian Lincoln Simon and Mary Lefkowitz, and called John Templeton Jr. a "sugar daddy" for such thinkers.

[89] Pamela Thompson, former Vice President of Communications of the foundation, replied that "the Foundation is, and always has been, run in accordance with the wishes of Sir John Templeton Sr, who laid very strict criteria for its mission and approach", that it is "a non-political entity with no religious bias" and it "is totally independent of any other organisation and therefore neither endorses, nor contributes to political candidates, campaigns, or movements of any kind".

[90] Drexel University sociologist Robert Brulle listed the foundation as among the largest financial contributors to the climate change denial movement between 2003 and 2010.