The combustion process in spark-ignition engines can vary considerably cycle by cycle, which may result in unstable engine operation. The phenomena amplify in natural gas (NG) spark-ignition (SI) engines due to the lower NG laminar flame speed compared to gasoline, and more so under lean burn conditions. The main goal of this study was to investigate the main sources and the characteristics of the cycle-by-cycle variation in heavy-duty compression ignition (CI) engines converted to NG SI operation. The experiments were conducted in a single-cylinder optically-accessible CI engine with a flat bowl-in piston that was converted to NG SI. The engine was operated at medium load under lean operating conditions, using pure methane as a natural gas surrogate. The CI to SI conversion was made through the addition of a low-pressure NG injector in the intake manifold and of a NG spark plug in place of the diesel injector. Flame luminosity images of the whole combustion event inside the piston bowl were used to analyze the major sources of cyclic variation. The optical measurements were combined with in-cylinder pressure measurements to infer the characteristics of the cycle-by-cycle variation. The results suggested that the spark intensity, arc continuity, and arc location affected the flame kernel inception. The gas motion and the mixture equivalence ratio around the spark location also influenced it. Then, the intake swirl and the turbulence during the compression stroke determined the flame propagation speed and direction. The variation in the fast burning between individual cycles compounded the cyclic variation caused by the ignition event. In addition, the reduction in flame propagation near the bowl wall decreased the cyclic variation. Moreover, the complex phenomena at the entrance of the squish region increased the cycle-by-cycle variations but it seems to not have a strong influence on the power output difference between cycles. Furthermore, the large surface-to-volume ratio in the squish region resulted in a large variation in the heat loss, then producing large differences in the flame development in the squish, which in turn affected the heat loss variation, and so on. But the COVIMEP was less than 4%, despite the extremely lean burn operation (ϕ = 0.66). It was probably due to the high turbulence intensity inside the bowl that helped with the rapid burning process inside the bowl. The strong turbulence was generated by the squish during the compression stoke. The reasonable COVIMEP suggest that the significant cycle-by-cycle variation in the burn inside the squish region had little impact on the COVIMEP. However, a large cycle-by-cycle variation in the squish burn would cause unstable CO and HC emissions, which is a concern for efficient engine operation.