Alves has been shown the exit door after just three months in charge of the 2009 KPL champions. His reign at the club started on a faulty ground after a season-opening loss to Posta Rangers at Narok Stadium.
They drew 2-2 against Kakamega Homeboyz in their last match at Bukhungu Stadium which proved to be the last game Alves oversaw Batoto ba Mungu.
Club legend John Baraza has been appointed to succeed his former boss Alves on a full-time basis.
"He [Alves] was not fired but he resigned as he handed me his resignation letter earlier. [John] Baraza will now take the coaching role officially," Elly Kalekwa, Sofapaka President told Goal.
Kalekwa further revealed Living 3D Holdings Limited, who were supposed to pay the tactician, raised some issues concerning Alves's salary.
"The people who were supposed to pay the coach brought up some issues but also his performance was very very poor," Kalekwa concluded.
This is Baraza's third time to return as head coach after he had replaced his former boss Sam Ssimbwa in the 2018 season. The Kenyan legend also replaced Melis Medo in January 2019.
Sofapaka are 12th on the log with just eight points.