In this paper, a methodology for designing and implementing a real time optimizing controller for non-linear batch processes is discussed. The controller is used to optimize the system input and state trajectories according to a cost function. An interior point method with penalty function is used to incorporate constraints into a modified cost functional, and a Lyapunov-based extremum seeking approach is used to compute the trajectory parameters. Smooth trajectories were generated with reduced computing time compared to many optimizations in literature. In this paper, the theory is applied to general non-flat non-linear systems in a true on-line optimization.