A transport refrigeration system (20) having: a multi-fuel capable engine (26); a refrigeration unit (22) powered by the engine (26); a first fuel system (120, 130, 140, 150) operably connected to the engine (26), the first fuel (120, 130, 140, 150) system including at least one of a propane fuel system (120), compressed natural gas fuel system (130), liquefied natural gas fuel system (140), and gasoline fuel system (150); a second fuel system (120, 130, 140, 150) operably connected to the engine (26), the second fuel system (120, 130, 140, 150) including at least one of a propane fuel system (120), compressed natural gas fuel system (130), liquefied natural gas fuel system (140), and gasoline fuel system (150); and a controller (30) configured to command a fuel to the engine (26) from the first fuel system (120, 130, 140, 150) or the second fuel system (120, 130, 140, 150), the controller (30) adjusts operation of the engine (26) in response to the fuel commanded. The first fuel system (120, 130, 140, 150) operates on a fuel different than the second fuel system (120, 130, 140, 150). Both fuel systems (120, 130, 140, 150) are separate modules being removably connected to the engine (26).