In Anglo-American discourse, he is perhaps best known in regard to his friendship with Friedrich Nietzsche; in German theological circles, Overbeck remains discussed for his own contributions.

During his student time in Leipzig, he became close friends with Heinrich von Treitschke, and in Göttingen, Overbeck had become a member of Burschenschaft Hannovera.

(Über die Christlichkeit unserer heutigen Theologie), in which he argued that the "historical" Christianity, as developed by the fathers of the church, neither did nor could have to do with the original ideas of Christ.

This work was primarily incited by David Strauss's The Old and New Faith (Vom alten und neuen Glauben, 1872) and Paul de Lagarde's 'On the Relationship of the German State to Theology, Church, and Religion' ('Über das Verhältnis des deutschen Staates zu Theologie, Kirche und Religion', 1873).

In his afterword for the second edition in 1903, he renewed this critique against theologian Adolf von Harnack and his work 'The Essence of Christianity' ('Das Wesen des Christentums', 1900).

In private, Overbeck made voluminous notes for a 'Church Lexicon' (Kirchenlexikon), in which he develops personal accounts, principally theological but also political, cultural, philosophical, and a literature bibliography with commentary.

To remain sincere to his friend, Overbeck maintained a critical distance from the content of Nietzsche's writings, and denounced the beginnings of a hero-worship and revisionism.

[citation needed] After long periods of sickness, in 1897 Overbeck became an emeritus professor, and in the following year, noticeably weakened, he gave up this honorary appointment at Basel.

Although a critical edition of Overbeck's publications (including many of his notes for his lexicon) has been published in Germany, few of his writings have been available in English translation until recently.