Dual fuel pilot-ignited natural gas engines are identified as an efficient and viable alternative to conventional diesel engines. This paper examines cyclic combustion fluctuations in conventional dual fuel and in dual fuel partially premixed combustion (PPC). Conventional dual fueling with 95% (energy basis) natural gas (NG) substitution reduces NOx emissions by almost 90% relative to neat diesel operation; however, this is accompanied by 98% increase in HC emissions, 10 percentage points reduction in fuel conversion efficiency (FCE) and 12 percentage points increase in COVimep. Dual fuel PPC is achieved by appropriately timed injection of a small amount of diesel fuel (2–3% on an energy basis) to ignite a premixed natural gas–air mixture to attain very low NOx emissions (less than 0.2 g/kWh). Cyclic variations in both combustion modes were analyzed by observing the cyclic fluctuations in start of combustion (SOC), peak cylinder pressures (Pmax), combustion phasing (Ca50), and the separation between the diesel injection event and Ca50 (termed “relative combustion phasing”). For conventional dual fueling, as NG substitution increases, Pmax decreases, SOC and Ca50 are delayed, and cyclic variations increase. For dual fuel PPC, as diesel injection timing is advanced from 20 deg to 60 deg BTDC, Pmax is observed to increase and reach a maximum at 40 deg BTDC and then decrease with further pilot injection advance to 60 deg BTDC, the Ca50 is progressively phased closer to TDC with injection advance from 20 deg to 40 deg BTDC, and is then retarded away from TDC with further injection advance to 60 deg BTDC. For both combustion modes, cyclic variations were characterized by alternating slow and fast burn cycles, especially at high NG substitutions and advanced injection timings. Finally, heat release return maps were analyzed to demonstrate thermal management strategies as an effective tool to mitigate cyclic combustion variations, especially in dual fuel PPC.