One of his book, Resistance of the Heart: Intermarriage and the Rosenstrasse Protest in Nazi Germany was co-recipient of the Fraenkel Prize in Contemporary History (1993). German and French translations carried a foreword by German Foreign Minister Joschka Fischer. In Britain it was a New Statesman "Book of the Year". Die Zeit called it the "standard work" on the protest, which was the center of a little Historikerstreit.

His other works include Social Outsiders in Nazi Germany (Princeton University Press, 2001), co-edited with Robert Gellately; Shades of Green: Environmental Activism around the Globe (Rowman & Littlefield, 2006), co-edited with Doug Weiner and Christof Mauch, Courageous Resistance: The Power of Ordinary People (Palgrave MacMillan, 2007), co-authored with five professors of history, political science, and sociology; Nazi Crimes and the Law (Cambridge University Press, 2008), co-edited with Henry Friedlander.

Nathan Stoltzfus is currently working on the impact of the Cold War and its demise on national memories and representations of WW II in several European countries.