A method of protecting a direct injection fuel injector in a multi-fuel engine, that comprises a plurality of cylinders, said method comprising: selectively operating said multi-fuel engine with a directly injected fuel introduced through said direct injection fuel injector and/or with a second fuel, and when fuelling said multi-fuel engine with said second fuel, selectively commanding a fuel system protection technique when determining that at least one of said direct injection fuel injectors requires cooling, wherein said fuel system protection technique comprises commanding that said directly injected fuel be a portion of total fuel consumed and reducing the quantity of said second fuel that is injected so that total fuel consumed equals a desired amount of fuel measured on an energy basis, wherein said determining is based on at least one of the following inputs: a temperature model for said direct injection fuel injector, an age of directly injected fuel is above a predetermined value, a transmission status has changed, an engine shutdown event has occurred, a driving pattern recognition predicts an engine shutdown event will occur. characterized in that said fuel system protection technique comprises: (a) co-fuelling one cylinder of said plurality of cylinders corresponding to an ignition firing event with said directly injected fuel and said second fuel, and fuelling the remaining of said plurality of cylinders with only said second fuel, (b) fuelling said plurality of cylinders corresponding to a predetermined number of subsequent ignition firing events with only said second fuel, and (c) repeating steps (a) and (b), wherein said cylinder that is co-fuelled is alternated with other ones of said plurality of cylinders whereby over time each cylinder is co-fuelled. selectively operating said multi-fuel engine with a directly injected fuel introduced through said direct injection fuel injector and/or with a second fuel, and when fuelling said multi-fuel engine with said second fuel, selectively commanding a fuel system protection technique when determining that at least one of said direct injection fuel injectors requires cooling, wherein said fuel system protection technique comprises commanding that said directly injected fuel be a portion of total fuel consumed and reducing the quantity of said second fuel that is injected so that total fuel consumed equals a desired amount of fuel measured on an energy basis, wherein said determining is based on at least one of the following inputs: a temperature model for said direct injection fuel injector, an age of directly injected fuel is above a predetermined value, a transmission status has changed, an engine shutdown event has occurred, a driving pattern recognition predicts an engine shutdown event will occur. characterized in that said fuel system protection technique comprises: (a) co-fuelling one cylinder of said plurality of cylinders corresponding to an ignition firing event with said directly injected fuel and said second fuel, and fuelling the remaining of said plurality of cylinders with only said second fuel, (b) fuelling said plurality of cylinders corresponding to a predetermined number of subsequent ignition firing events with only said second fuel, and (c) repeating steps (a) and (b), wherein said cylinder that is co-fuelled is alternated with other ones of said plurality of cylinders whereby over time each cylinder is co-fuelled. a temperature model for said direct injection fuel injector, an age of directly injected fuel is above a predetermined value, a transmission status has changed, an engine shutdown event has occurred, a driving pattern recognition predicts an engine shutdown event will occur. characterized in that said fuel system protection technique comprises: (a) co-fuelling one cylinder of said plurality of cylinders corresponding to an ignition firing event with said directly injected fuel and said second fuel, and fuelling the remaining of said plurality of cylinders with only said second fuel, (b) fuelling said plurality of cylinders corresponding to a predetermined number of subsequent ignition firing events with only said second fuel, and (c) repeating steps (a) and (b), wherein said cylinder that is co-fuelled is alternated with other ones of said plurality of cylinders whereby over time each cylinder is co-fuelled. (a) co-fuelling one cylinder of said plurality of cylinders corresponding to an ignition firing event with said directly injected fuel and said second fuel, and fuelling the remaining of said plurality of cylinders with only said second fuel, (b) fuelling said plurality of cylinders corresponding to a predetermined number of subsequent ignition firing events with only said second fuel, and (c) repeating steps (a) and (b), wherein said cylinder that is co-fuelled is alternated with other ones of said plurality of cylinders whereby over time each cylinder is co-fuelled.