A control system for controlling pilot fuel injection in a dual fuel engine is disclosed. The control system may determine, using measurements from one or more sensors, one or more combustion parameters associated with the dual fuel engine during operation of the dual fuel engine. The control system may determine an estimated nitrogen oxides (NOx) emissions level based on the one or more combustion parameters, and may determine a NOx error based on a comparison between the estimated NOx emissions level and a desired NOx emissions level. The control system may control a quantity of pilot fuel injected into the dual fuel engine based on the NOx error.