A method of protecting a direct injection fuel injector in a multi-fuel engine, the method includes selectively operating the multi-fuel engine with a directly injected fuel introduced through the direct injection fuel injector and a second fuel; when fuelling the multi-fuel engine with the second fuel, selectively commanding a fuel system protection technique when determining that the direct injection fuel injector requires cooling, an age of directly injected fuel is above a predetermined value, transmission status has changed, an engine shutdown event has occurred and a global positioning system signal indicates an engine shutdown event will occur; wherein the fuel system protection technique includes commanding that the directly injected fuel be a portion of total fuel consumed and reducing quantities of the second fuel that is injected so that total fuel consumed equals a desired amount of fuel measured on an energy basis.