He was executed by the Communist-led Yugoslav Partisans for his collaboration with occupying Axis powers during World War II.

Metropolitan Joanikije attempted to maintain the diocese as the area transitioned between German and communist rule.

With the ascendancy of communist control he attempted to leave the area with a number of his priests.

Joanikije collaborated with occupying Axis forces and supported the activities of the Serbian Chetniks.

He was at the head of the column of Montenegrin Chetniks which attempted to flee Yugoslavia through Germany at the end of the war.