Schäfer contends that Philo's logos was likely derived from his understanding of the "postbiblical Wisdom literature, in particular the Wisdom of Solomon." In 2018 Schäfer was criticized for inviting a Palestinian scholar to give a lecture at the museum and giving a personal tour to the cultural director of the Iranian embassy. In 2019 he was pressured to resign from his position as director of Berlin's Jewish Museum because of a Twitter post by the museum that allegedly implied support of the Boycott, Divestment and Sanctions movement.
Major books
Schäfer's books contribute to the understanding of classical Judaism as well as ancient Jewish and Christian relations:
Judeophobia: Attitudes toward the Jews in the Ancient World, Harvard University Press, 1998. This has been translated into several languages.
Jesus in the Talmud, Princeton University Press, 2007.
The Origins of Jewish Mysticism, Princeton University Press, 2009.
The Jewish Jesus: How Judaism and Christianity shaped each other, Princeton University Press, 2012.
Landmark synoptic editions
Schäfer has encouraged the study of esoteric subjects in early Judaism through the publication of synoptic editions of ancient texts. These editions collate multiple manuscripts in large-format books that allow for line by line comparison of ancient Hebrew and Aramaic texts.
Hekhalot literature: Synopse zur Hekhalot-Literatur. Tübingen: J.C.B. Mohr, 1981.
Sefer Ha-Razim: Peter Schäfer and B. Rebiger. Sefer ha-Razim. Tübingen: Mohr Siebeck, 2009.
Toledot Yeshu: Peter Schäfer and Michael Meerson with the collaboration of Yaacov Deutsch, David Grossberg, Avigail Manekin, and Adina Yoffie. Toledot Yeshu: the Life Story of Jesus. Tübingen: Mohr Siebeck, 2014.
Other works
Peter Schäfer, Die Vorstellung vom heiligen Geist in der rabbinischen Literatur, Munich 1972
Peter Schäfer, Rivalität zwischen Engeln und Menschen : Untersuchungen zur rabbinischen Engelvorstellung. Berlin de Gru.75.
Peter Schäfer, Geschichte der Juden in der Antike. Die Juden Palästinas von Alexander dem Großen bis zur arabischen Eroberung, Catholic Publishers, Stuttgart, 1983 in: Journal for the Study of Judaism, Volume 14, Number 2, 1983, pp. 221–224
Peter Schäfer, Irina Wandrey: Reuchlin und seine Erben : Forscher, Denker, Ideologen und Spinner, Thorbecke 2005,
Peter Schäfer and Elisabeth Müller-Luckner: Wege mystischer Gotteserfahrung: Judentum, Christentum und Islam, Oldenbourg Munich 2006,
Peter Schäfer: Jesus im Talmud, Mohr Siebeck Tübingen 2007,, translated Barbara Schäfer: Jesus in the Talmud, Princeton University Press 2007,
The Bar Kokhba War Reconsidered: Archaeological, Historical, and Literary Perspectives on the Second Jewish Revolt against Rome, Tuebingen 2003
Der Triumph der reinen Geistigkeit. Sigmund Freuds "Der Mann Moses und die monotheistische Religion", Berlin and Vienna 2003.