Troughton lasted only two games with All Stars after taking over the coaching reins from former Mamelodi Sundowns goalkeeper Calvin Marlin.
The former Pretoria Callies coach has returned home to Tshwane and is waiting for offers for next season.
Troughton has since explained the reasons for his departure from the Cape side.
"It was going to take me a long time to apply my philosophy and I agreed with the club chairman to leave and probably come back next season," Troughton tells snl24.com/kickoff.
"The club was facing relegation and felt Calvin Marlin could continue and try to help the club to survive."
All Stars have since secured their status in the GladAfrica Championship for next season as neighbours Steenberg United and Cape Town Spurs remain fighting for survival.