Soon after taking the position of metropolitan, the April War brought the World War II to Yugoslavia and resulted in the establishment of the Italian governorate of Montenegro. 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. Joanikije was captured by Yugoslav Partisans on May 12 near Celje and taken to Zagreb. On orders from Milovan Đilas, he was transferred to Belgrade. He and his party were executed by the Partisans at Bukovik near Aranđelovac on 18 June 1945.