A method for controlling mode transitions, such as from stratified to homogeneous mode, in a direct injection engine adjusts an intake manifold outlet control device, such as a cam timing, to rapidly control cylinder fresh charge despite manifold dynamics. In addition, a coordinated change between an intake manifold inlet control device, for example a throttle, and the outlet control device is used to achieve the rapid cylinder fresh charge control. In this way, engine torque disturbances during the mode transition are eliminated, even when cylinder air/fuel ratio is changed from one cylinder event to the next.