Bishop Jovan became a central figure in the long-standing dispute between the Macedonian Orthodox Church (MPC) and the Serbian Orthodox Church (SPC) when he switched allegiance from MPC to the SPC in 2003.

He was arrested in January 2004 for "conducting illegal religious services on non-church land" and was sentenced on 19 August by a court in Bitola for inciting religious and ethnic hatred.

Prosecutors also charged that he published calendars and other religious literature that allegedly slandered the MPC.

The central problem is deeply rooted in what historians call the Macedonian Question and interrelated issues involving the traditional Balkan tendency to equate one's nationality with one's religion. In 1967, the communist Macedonian authorities recognized a MPC separate from the SPC and the Bulgarian Orthodox Church, which has a much smaller number of Macedonian adherents than the other two. The SPC and other Orthodox churches do not recognize their Macedonian counterpart, regarding it as schismatic.