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The monastery is believed to have been built when Saint Clement arrived in Ohrid, at the request of Boris I of Bulgaria and restored an old church. Sources say that Saint Clement was not satisfied with the size of the church and therefore built a new one over it and assigned Saint Panteleimon as its patron saint.

Saint Clement used his newly created monastery as a liturgical building and a place for teaching his disciples his variation of the Glagolitic alphabet, known as the Cyrillic alphabet. Clement personally built a crypt inside the monastery in which he was buried after his death in 916, his tomb still exists today.

In the 15th century, Ottoman Turks converted the monastery into a mosque but during the beginning of the 16th century allowed ruined churches and monasteries to be restored, therefore, so was Saint Clement's monastery. The monastery was again ruined during the end of the 16th century or the beginning of the 17th century and yet another mosque, called Imaret Mosque, was erected by the Ottomans, this mosque still exists to this day.[1]