An engine control system includes a dual fuel internal combustion engine, a fuel system including a liquid fuel source and a gaseous fuel source, and a controller. The engine control system further includes a liquid fuel control module and at least one gaseous fuel control module associated with a first and second subset of cylinders, each communicatively connected over a network. The controller has an operating mode and a cylinder deactivation mode. The controller in the operating mode is configured to instruct the liquid fuel control module and the at least one gaseous fuel control module to operate the plurality of cylinders in a dual fuel mode. The controller in the cylinder deactivation mode transitions the plurality of cylinders to a liquid-fuel only mode over a phase out period, deactivates the first subset of cylinders, and then transitions to the dual fuel mode in the second subset of cylinders.