Decades of work on low-carbon fuels have established their potential for substantial emissions reductions; however, their adoption is still limited by infrastructure concerns and engine efficiency deficits. As infras-tructures have begun to evolve, research on strategies that maximize engine efficiency through interactions with fuel properties must also now take center place. This paper compares the performance, emissions, and combustion characteristics of two forefront low-carbon fuels: compressed natural gas (CNG) and liquefied petroleum gas (LPG) in a cooperative fuel research (CFR) engine over a range of compression ratios and engine loads. The effects of exhaust gas recirculation (EGR), end-gas auto-ignition, and a novel combustion control tool, the combustion intensity metric (CIM), were also evaluated at different stoichiometric engine operating conditions. In comparison to LPG, CNG operation demonstrated an extended knock-free regime, allowing engine operation at higher engine loads and compression ratios, but LPG operation exhibited enhanced combustion characteristics with higher peak pressures and faster apparent heat release rates (AHRR). LPG operation achieved higher brake thermal efficiencies and lower equivalent CO2 emissions compared to CNG operation at the tested engine loads and compression ratios. LPG demonstrated significantly higher EGR tolerance limits compared to CNG, with a maximum of 28% EGR rate, compared to 23% for CNG. This improved EGR dilution tolerance was responsible for a 90% reduction in NOx emissions for LPG compared to a maximum of 70% with CNG. EGR dilution also exhibited more effective knock mitigation potential with LPG, suppressing knock intensity values by up to 98% and transitioning the engine operation towards normal combustion from heavy knocking conditions. The CIM was found to decrease burn durations and improve the quality of combustion by controlling the desired fraction of end-gas auto-ignition.