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 [[monasticism|monastic]] vows, was tonsured a [[monk]] with the name Jovan (John), and was [[ordination|ordained]] a [[deacon]]. The following day, [[February 8]], he was ordained to the [[priest]]hood, becoming a [[hieromonk]]. On [[July 19]], 1998, Fr. John was [[consecration of a bishop|consecrated]] a [[bishop]] with the title of Bishop of Dremvica and assigned as [[auxiliary bishop|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 [[schism]]atic Macedonian Orthodox Church formed. Leading the Holy Metropolitanate of Veles and Vardar Valley, on [[June 22]], 2002, Metr. John responded to the summons for liturgical and canonical unity with the Patriarchate of Peć by the [[Patriarch]] of [[Church of Serbia|Serbia]], [[Pavel (Stojcevic) 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.