The former Ayr United boss had been in charge at Hampden since September 2018, when he took over from Gus MacPherson.
Roberts and assistant Robert Walker have now left the League 2 club - who are seventh in the table - by mutual consent and coach Tony Quinn will take charge for Saturday's home game against Stenhousemuir.
President Gerry Crawley said: “I would like to thank Mark and Robert for their service and commitment during their time at Queen’s Park and wish them every success in the future."
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