He was born on February 28, 1966 in Bitola, Yugoslavia and baptized as an Orthodox Christian named Zoran. He completed his primary school and mathematical high school in his native town, receiving many awards for achievements in the fields of science and sports. In 1985, after having served his military obligation in Sarajevo, he began studies at the Faculty of Civil Engineering in Skopje, graduating in 1990.
Later in 1990, he enrolled the Faculty of Theology in Belgrade while working as a civil engineer with the Metropolitanate of Bitola. While employed by the metropolis, he established its library in collaboration with the local University Library of Bitola, while serving also as the new library's first librarian. During his two and half years in this position the young Zoran gave a series of lectures.
In 1993, he left Bitola for Belgrade to continue his studies in theology, graduating in June 1995. Immediately, he began his master's studies at the Department of Systematic Theology (Dogmatics). At the end of 1995, he moved to Thessalonica in Greece to learn Greek and enroll for postgraduate studies. In Thessalonica, he worked on his doctorate and a dissertation entitled: The Unity of the Church and the Contemporary Ecclesiological Problem.
On February 7, 1998, he took monastic vows, was tonsured a monk with the name Jovan (John), and was ordained a deacon. The following day, February 8, he was ordained to the priesthood, becoming a hieromonk. On July 19, 1998, Fr. John was consecrated a bishop with the title of Bishop of Dremvica and assigned as vicar to the Bishop of Prespa and Pelagonia. In this position, and in addition to taking part theological consultations, Bp. John led the effort for reconstruction of the Cathedral Church of St. Great Martyr Demetrius in Bitola. In March 2000, he was assigned as administrator of the Metropolitanate of Bregalnica. In November 2000, Bp. John was elected Bishop of Veles and Vardar Valley and enthroned on December 4 2000.
With the separation of the member states of Yugoslavia after the fall of communism, Macedonia also declared its independence and a schismatic Macedonian Orthodox Church formed. Leading the Holy Metropolitanate of Veles and Vardar Valley, on June 22, 2002, Metr. John responded to summon for liturgical and canonical unity with the Patriarchate of Pec by Patriarch of Serbia, Pavle. Together with all his clergy and faithful of his Metropolitanate, Metr. John was the only Bishop of the schismatic Macedonian Orthodox Church who responded positively.
A few days later, he was expelled from the seat of the Metropolitanate together with the monastic community living with him. This was done illegally and without a court warrant by the Police of the Republic of Macedonia. On September 23, 2002, Metr. John was appointed Exarch of all the territories of the Ohrid Archdiocese by the Assembly of the Serbian Orthodox Church. On December 25, 2003, he was elected Chairman of the Holy Synod of Bishops of the Orthodox Ohrid Archdiocese, after it had been constituted.
He was detained under custody many times by the authorities of the Republic of Macedonia. He was sentenced to a suspended punishment one year of imprisonment for the criminal offense of «"performing unauthorized activities" because he had entered a church to baptize a female infant in 2004. The Court of Appeal in Bitola sentenced him to eighteen months of imprisonment in 2005 as judgment for a criminal offense of "incitement of ethnic and religious hatred, discord and intolerance".
On May 24, 2005, on the Feast of the Ss. Cyril and Methodius, he was confirmed by his Holiness, the Archbishop of Pec, Metropolitan of Belgrade and Karlovci, and Patriarch of Serbia, Pavle, to be Archbishop of Ohrid and Metropolitan of Skopje in accordance with the Niš Agreement. On the same day, there was an announcement of the Patriarchal and the Assembly's Tomos for Autonomy of the Ohrid Archdiocese, with Metr. John as the Chairman of the Holy Synod of Bishops.