Methods and systems of controlling operation of a dual fuel engine are provided, comprising determining a target exhaust temperature, sensing an actual exhaust temperature, determining an exhaust temperature deviation by comparing the actual exhaust temperature to the target exhaust temperature, comparing the exhaust temperature deviation to a threshold, adjusting at least one of an intake throttle, a wastegate, a compressor bypass valve, an exhaust throttle, a VGT and engine valve timing when the exhaust temperature deviation exceeds the threshold to control charge-flow to the engine, and continuing the adjusting until the exhaust temperature deviation is less than the threshold.