A fuel injection timing management system for a dual fuel engine is configured to determine a first diesel injection timing corresponding to a first mode of operation of the engine system and a second diesel injection timing corresponding to a second mode of operation. The system may further determine a direction of change in a mode of operation of the engine system, and selectively perform a change in the diesel injection timing from the first diesel injection timing to the second diesel injection timing at a first rate of transition or a second rate of transition, based on the direction of change in a mode of operation of the engine system.