In the 1990s, Groothuis began to write about the cultural shifts associated with postmodern philosophy in his book Truth Decay, as well as to formulate responses to those shifts via Christian apologetics. He was also interested in human behavior and belief associated with the use of the Internet, and wrote of his theological concerns in The Soul in Cyberspace. His interests in philosophy have also led him to write on topics like Immanuel Kant's epistemology, the rationality of theism, and book-length treatments of the philosophical ideas and methods of Blaise Pascal and Jesus. In 2011, Groothuis published a comprehensive textbook on Christian apologetics.
