Mokwena has spent the past few months at Chippa United after he was loaned to the Port Elizabeth club but only managed to take charge of one game due to the coronavirus-enforced suspension of football.
"He signed the same number of years with Micho," an insider tells snl24.com/kickoff.
"The club will not retain him when his contract expires at the end of the season."
Mokwena joined Pirates together with former head coach Milutin Sredojevic three years ago.
'Micho' only spent two seasons with The Buccaneers before leaving the country to join Zamalek in Egypt.
Efforts to get hold of Bucs administration official Floyd Mbele to comment on the future of Mokwena proved futile.