Motion is coordinated between a robot and a mover in an independent cart system. Positions for a mover along a track for the independent cart system and for each axis of motion of the robot mounted on the mover are received at the motion controller. The axis position corresponds to either an angular position of the motor or a mechanical position of a corresponding axis on which the motor is mounted. The motion controller receives a robot motion command corresponding to a desired operation of the robot and generates a mover motion command for the mover and an axis motion command for each axis of the robot. The mover motion command and the axis motion commands are generated as a function of the robot motion command, the position of the mover along the track, and the position of the motor or of the axis for each axis of the robot.