A controller of a quantum system identifies a phase update trigger for a quantum object of the quantum system and an interaction time. Responsive to identifying the phase update trigger, the controller determines, for between a first time and the interaction time, (a) a location/transport effect on a phase of the quantum object based on locations thereof and transport operations performed thereon, and (b) a quantum operation effect on the phase of the quantum object based on any quantum operations applied thereto. The immediately previous phase update for the quantum object occurred at the first time. Based on the location/transport effect, the quantum operation effect, and the interaction time, the controller determines an interaction time phase of the quantum object. The controller adjusts operation of a manipulation source such that a phase of a signal generated by the manipulation source corresponds to the interaction time phase at the interaction time.