Converting existing diesel engines to the spark ignition (SI) operation can increase the utilization of natural gas (NG) in heavy-duty applications, which can reduce oil imports in the US and curtail greenhouse-gas emissions. The NG operation at lean-burn conditions was evaluated inside a retrofitted heavy-duty direct-injection compression-ignition (CI) engine, where the diesel injector was replaced with a high-energy spark plug and NG was mixed with air in the intake manifold. Steady-state engine experiments that changed combustion phasing were performed at 13.3 compression ratio, lean equivalence ratio, medium load, and low-speed conditions, fueled with pure methane as NG surrogate. Results suggested that NG combustion inside such retrofitted engines is different from that in conventional SI engines due to the geometric characteristics of the diesel combustion chamber. In detail, the different conditions inside the bowl and the squish partitioned the combustion process into two distinct events in terms of timing and location. Moreover, the squish region helped stabilize the extreme lean operation by creating a highly turbulent flow into the bowl during the compression stroke. However, combustion efficiency and unburned hydrocarbon emissions were significantly affected by the fuel fraction that burned inside the squish region under less than optimal conditions during the expansion stroke. As a result, despite the combustion phasing being the primary control of engine’s indicated thermal efficiency, the combustion strategy for CI engines converted to NG SI should optimize the slower burning inside the squish region.