Muñoz is Tocqueville Associate Professor of Religion & Public Life in the Department of Political Science at the University of Notre Dame. He is also the director of the Tocqueville Program for Inquiry into Religion and Public Life and the Potenziani Program in Constitutional Studies. In March 2017, Muñoz invited Charles Murray to campus despite opposition from junior faculty and students; he argued that Murray's presence would signal that Notre Dame is a safe space for free speech. Muñoz authored God and the Founders: Madison, Washington, and Jefferson in 2009. The book analyzes the different positions on church and state of three Founding Fathers and contextualizes them in modern-day judicial conundra like school prayers or public funding of religious institutions. It won the Hubert Morken Award from the American Political Science Association in 2011. The book was widely reviewed. In Perspectives on Politics, Professor Isaac Kramnick of Cornell University, called it a "very important book", although he regretted Muñoz's decision to look at only three founders, concluding that other founders could illuminate modern-day jurists further. Meanwhile, in Law and History Review, Professor Mark D. McGarvie of the College of William and Mary argued that the ahistorical nature of the analysis was problematic, but that the book was nevertheless engaging. Professor Ellis M. West of the University of Richmond dismissed the book for lacking "balance and nuance", despite recognizing that Muñoz is correct to argue that "none of the Founders believed that religious liberty gave people the right to be exempt from obeying valid laws that unintentionally burden the exercise of their religion." Furthermore, in Revue française de science politique, Professor François Foret of the Université libre de Bruxelles praised Muñoz for laying out the differences between the Founders. Finally, in a review for the Journal of the Early Republic, Professor Mark Y. Hanley of Truman State University praised the book for "granting the founders their separate ways while acknowledging the continuing vitality of their political and philosophical ideas that can still offer Constitutional guidance in a new century." Muñoz edited a second book, Religious Liberty and the American Supreme Court: The Essential Cases and Documents, in 2015. It is a collection of Supreme Court cases on religious liberty, with annotations by Muñoz.
