Steinberger's first marriage to Joan Beauregard ended in a divorce, after which he married his former student and biologist, Cynthia Alff. He had four children, two from each of his marriages. His son Ned Steinberger is the founder of the eponymous company for headless guitars and basses, and his daughter Julia Steinberger is an ecological economist at the University of Lausanne. As an atheist and a humanist, Steinberger was a Humanist Laureate in the International Academy of Humanism. In his own words, he is noted to have enjoyed tennis, mountaineering and sailing.