Embodiments of the invention can provide systems and methods for using a combustion dynamics tuning algorithm with a multi-can combustor. According to one embodiment of the invention, a method for controlling a gas turbine engine with an engine model can be implemented for an engine comprising multiple cans. The method can include obtaining operating frequency information associated with multiple cans of the engine. In addition, the method can include determining variation between operating frequency information of at least two cans. Furthermore, the method can include determining a median value based at least in part on the variation. Moreover, the method can include determining whether the median value exceeds at least one operating threshold. The method can also include implementing at least one engine control action to modify at least one of the operating frequencies if at least one operating threshold is exceeded.