Wells was born in New York City in 1942 and grew up in New Jersey, and was brought up as a Protestant Christian. He studied geology at Princeton University, where he dropped out in his junior year. Following a brief stint as a taxi driver, he was drafted by the army and spent two years serving in Germany. After his discharge in 1966, he attended University of California, Berkeley, where he publicly refused to report for reserve duty. This resulted in him being arrested and being incarcerated for 18 months at the Leavenworth military prison. Upon his release, Wells returned to Berkeley where he completed his studies with a major in geology and physics and a minor in biology Jonathan Wells has received two Ph.D.s, one in Molecular and Cell Biology from the University of California at Berkeley, and one in Religious Studies from Yale University. He has worked as a postdoctoral research biologist at the University of California at Berkeley and the supervisor of a medical laboratory in Fairfield, California, and he has taught biology at California State University East Bay in Hayward, California.

In 1974 Wells joined the Unification Church. He graduated from the church's Unification Theological Seminary in 1978 with a Masters in Religious Education. Wells continued his studies at Yale University, earning a PhD in religious studies in 1986, focusing on historical reactions to Darwinism. During this time he wrote extensively on Unification theology and taught at the Unification Theological Seminary. Wells was on the Board of Trustees of the Unification Theological Seminary until resigning in 1997 to return to teaching. He also acted as the director of the International Religious Foundation, a Unification Church affiliated organization which sponsors interdenominational conferences.

Wells has written on the subject of marriage within the Unification Church and has been called a "Unification Church marriage expert" by church sources. Wells defended Unification Church theology against what he said were unfair criticisms made in 1977 by the National Council of Churches.

In 1994 Wells earned another PhD in Molecular and Cell Biology from UC Berkeley. After receiving his doctorate, he worked at a position he described as "a post-doctoral research biologist at Berkeley, writing articles critical of Darwinism.” Shortly after that Wells joined former UC Berkeley law professor Phillip E. Johnson, father of the intelligent design movement, at the Discovery Institute. He now serves as a fellow at the Discovery Institute's Center for Science and Culture, hub of the intelligent design movement, and at the International Society for Complexity, Information and Design, which also promotes intelligent design.

Dr. Wells is currently working on a book criticizing the over-emphasis on genes in biology and medicine..

Of his student days at Unification Theological Seminary (1976—78), Wells said, "One of the things that Father [Reverend Sun Myung Moon] advised us to do at UTS was to pray to seek God's plan for our lives." He later described that plan: "To defend and articulate Unification theology especially in relation to Darwinian evolution."

Wells stated that his religious doctoral studies at Yale, which were paid for by the Unification Church, focused on the "root of the conflict between Darwinian evolution and Christian doctrine" and encompassed the whole of Christian theology within a focus of Darwinian controversies. He said:

Wells said that "destroying Darwinism" was his motive for studying Christian theology at Yale and going on to seek his second Ph.D. at Berkeley, studying biology and in particular embryology:

Wells has written articles for the Discovery Institute, WorldNetDaily, Origins & Design, and other sympathetic publications attacking evolution and defending intelligent design. In 1997 he presented a paper entitled "Evolution by Design" at the Unification Church sponsored International Conference on the Unity of the Sciences in Washington D.C.. In 1999 he debated with the New Mexicans for Science and Reason. He was one of the contributors to Natural History Magazine's 2002 debate between ID advocates and evolution supporters.

In 2005 he debated Massimo Pigliucci on the PBS talk show Uncommon Knowledge. Pigliucci said Wells that "clearly lied" during his debates and misrepresented his agenda and science, as well as not understanding some of the theories he tries to attack.

Wells is one of the signatories of the Discovery Institute's "A Scientific Dissent From Darwinism", a controversial petition which the intelligent design movement uses to promote intelligent design by attempting to cast doubt on evolution.

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