At the urging of his father, most of his siblings also followed a religious career, the exceptions being his two oldest brothers Charles I and Bernard II and his sister Margaret.

In 1459, Diether von Isenburg was elected Archbishop of Mainz, ahead of Adolph II of Nassau by a narrow margin.

By appointing Johann, John II thwarted the intentions of Archbishop Rupert of Cologne, who had a different reform candidate in mind.

In 1488, John II of Baden waged a feud against Cuno III von Winneburg and Beilstein and in 1497 he had 12,000 men besiege the city of Boppard, which was trying to regain its imperial freedom.

John II died in 1503 in Ehrenbreitstein (now part of Koblenz), after a tenure of 46 years, 7 months and 18 days, the longest of any bishop of Trier.