He was born on 20 April 1959 into the Banjani tribe in the village of Velimlje near the city of Nikšić. Through his maternal family he is related to Arsenije IV Jovanović Šakabenta.[5] He finished his secondary education at the Nikšić Gymnasium. He graduated from the University of Belgrade Faculty of Orthodox Theology in 1990 and he finished his advanced studies at the University of Belgrade Faculty of Philosophy.[2] He was ordained a monk in the Ćelija Piperska Monastery on 30 October 1990. He was ordained a hierodeacon on 7 February 1991 and a hieromonk on 17 February 1991, taking the role of caretaker head of the Savina Monastery. On 1 September 1991 he became the head of the Cetinje Monastery and a teacher and main instructor in the re-formed Cetinje Seminary. In September 1995, he was promoted to the rank of protosyncellus and he was placed as the caretaker rector of the Cetinje Seminary.[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.[7][8]
On 12 May 2020, in the course of the mass manifestations against the proposed "Law on Freedom of Religion or Belief and the Legal Status of Religious Communities", Bishop Joanikije was arrested by Montenegrin police for leading a religious procession marking the day of Saint Basil of Ostrog.[9] On 16 May 2020, Bishop Joanikije and eight priests of the Orthodox Cathedral of St. Basil of Ostrog in Nikšić were released at around midnight after 72 hours spent in detention.[10]
On 3 November 2020 Joanikije tested positive to COVID-19. His health had improved in the meantime, and on 28 November, the results of the tests performed showed that he was negative for COVID-19.[13]
On 5 September 2021, he was enthroned in the Cetinje Monastery by Patriarch Porfirije. 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]Violent protests had begun the day prior with predominantly Montenegrin nationalist protesters setting up barricades at the town′s entrance in order to prevent the Patriarch and Metropolitan from reaching the monastery.[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.[16] No fewer than 20 people were injured and police arrested more than a dozen people, including the security advisor to president Milo Đukanović, Veselin Veljović.[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".[17][19]