Nobody was ever in any doubt that he was a priest. He married the very powerful widow of
his brother Aristobulus, Alexandra Salome, who gave him the titles of High Priest and
King.
His problem was that he was more interested in ruling as a
king, on the Greek model, than in being a priest. He didn't observe the rituals as the Pharisees thought he should, and this was a major contributor to the outbreak of civil war. He may have changed
his coin inscriptipon to Yonatan to appease them (he certainly followed a much more pro-Pharisee policy after a negotiated
peace), but nobody really knows.