After studying at the University of Cologne, in 1520 Gnapheus became dean of a Latin school in The Hague, where he encountered Reformation ideas.
When in 1523 he and Cornelis Hoen were arrested, he met Jan de Bakker (Johannes Pistorius), the first Protestant martyr (1525) in the Netherlands.
While there, Gnapheus was involved in a carnival play which mocked Prince-Bishop Mauritius Ferber, Nicolaus Copernicus and other Catholic clergy of the neighboring Prince-Bishopric of Ermeland.
Since 1537, Johannes Dantiscus, Ferber's successor as prince-bishop, spoke out against Gnapheus, who had to move on to the court of Duke Albert of Prussia in Königsberg (Królewiec).
Gnapheus served as tutor for Countess Anna of Oldenburg, consort in East Frisia, in Norden until his death in 1568.