On the recommendation of Amfilohije, the Bishops' Council during its regular session in May 2000 re-established the old Eparchy of Budimlja and Nikšić.

[2] In December 2019, Bishop Joanikije survived an assassination attempt in Belgrade, Serbia,[6] while he was in a meeting with Montenegrin-Serbian businessman and Church benefactor Miodrag Davidović.

On 1 November, Joanikije was one of speakers at the funeral of Metropolitan Amfilohije, in the Cathedral of the Resurrection of Christ in Podgorica, along with Serbian Patriarch Irinej, notable poet and Amfilohije's close friend Matija Bećković and Prime Minister of Montenegro, Zdravko Krivokapić.

The decision to hold the ceremony at a historic monastery in the town of Cetinje, the country′s former capital, further exacerbated political and ethnic tensions in Montenegro.

[15] Both the Metropolitan and the Patriarch were flown to Cetinje by helicopter and then led into the monastery by heavily armed riot police holding bulletproof vests over their bodies to protect them, as riot police used tear gas to disperse protesters who hurled rocks and bottles at them and fired guns into the air.

[15][17][18] Đukanović, who had recommended that the inauguration of Joanikije be held elsewhere and encouraged the protesters to disrupt the ceremony, stated that "Today we witnessed the embarrassment of both the Church and the government", while prime minister Zdravko Krivokapić called the violence an "attempted act of terrorism".