Increasing the natural gas (NG) use in heavy-duty engines is beneficial for reducing greenhouse-gas emissions from power generation and transportation. However, converting compression ignition (CI) engines to NG spark ignition operation can increase methane emissions without expensive aftertreatment, thereby defeating the purpose of utilizing a low carbon fuel. The widely accepted explanation for the low combustion efficiency in such retrofitted engines is the lower laminar flame speed of natural gas. In addition, diesel engine’s larger bowl size compared to the traditional gasoline engines increases the flame travel length inside the chamber and extends the combustion duration. However, optical measurements performed in this study suggested that a fast-propagating flame was developed inside the cylinder even at extremely lean operation. This was supported by a three-dimensional numerical simulation, which indicated that the squish region of the bowl-in-piston chamber generated a high turbulence intensity inside the bowl. However, the flame propagation experienced a sudden 2.25x reduction in speed when transiting from the bowl to the squish region. Such a phenomenon was caused by the large decrease in the turbulence intensity inside the squish region during the combustion process. Moreover, the squish volume trapped an important fuel fraction, and it is this fraction that experienced a slow and inefficient burning process during the expansion stroke. This resulted in increased methane emissions and reduced combustion efficiency. Overall, it was the specifics of the combustion process inside a bowl-in-piston chamber not the methane’s slow laminar flame speed that contributed to the low methane combustion efficiency for the retrofitted engine. The results suggest that optimizing the chamber shape is paramount to boost engine efficiency and decrease its emissions.