Receiving a dispensation from the regulations concerning canonical age, he was ordained priest and stationed at Reichenhall, Saalfelden, and Passau, where his clerical activity soon found great approbation.

Suspected of Lutheran heresy, he went to Wittenberg in 1523, where he was cordially welcomed by Martin Luther, Philip Melanchthon, and Bugenhagen.

The Elector August likewise sought formal expressions of opinion from Pfeffinger; and in this connection, in 1555, he proposed, with a view to securing religious uniformity, that the Interim liturgy of 1549 should again be used.

Against Nicolaus von Amsdorf he wrote his Antwort (Wittenberg, 1558), Demonstratio mendacii (1558), and Nochmals grundlicher Bericht; while he opposed Matthias Flacius in his Verantwortung.

He embodied his tenets in five articles of the Formula der Bekendnus of June 3, 1556, which he also submitted, in amplified form, to the Wittenberg theologians.