A method for controlling fuel flow in a multi fuel engine is disclosed. An input power for operating the multi fuel engine at a desired engine speed is determined and a fuel flow rate based on the input power, one or more fuel properties and a specified fuel substitution ratio for apportioning the plurality of fuels is determined. Also, a correction factor for the fuel flow rate based on a desired charge density, wherein the desired charge density is based at least on a relationship between an engine load and charge density is determined and a corrected fuel flow rate, based on the determined correction factor, is output to a corresponding actuator of a fluid flow control device for the one of the fuels to cause the corresponding actuator to provide the one of the plurality of fuels at the corrected fuel flow rate.