As energy security and sustainability becomes important, the role of alternative fuels, particularly methanol, is becoming increasingly significant. While the feasibility of methanol as a substitute for diesel fuel has been explored, understanding of emissions from methanol-fueled compression-ignition engines remains limited, even though these engines are known to emit formaldehyde (CH2O) due to methanol’s chemical structure and oxidation pathways. In this study, a quantitatively measurable mid-IR laser-based extinction methodology was employed to understand CH2O formation in a methanol mixing-controlled compression ignition (MCCI) engine. Stable methanol MCCI combustion was achieved with the addition of 5%vol 2-ethylhexly nitrate (EHN) and by using a triple injection strategy (pilot + pilot + main), and CH2O emissions were measured with high temporal resolution by laser extinction while sweeping the injection timing. In addition, the injection strategy was systematically varied by enabling and disabling different injection events to investigate the effect of pilot and main injections on CH2O formation. Injection timing sweeps revealed that CH2O emissions did not monotonically increase with retarded injection, as carbon monoxide did. This decoupling suggests that CH2O formation is not governed solely by global combustion inefficiencies but is instead tied to localized mixture conditions and oxidation pathways. Cycles with elevated CH2O emissions featured minimal low-temperature heat release of pilot injections and, subsequently, more retarded combustion phasing. This indicates that combustion quality of pilot injections strongly affect engine-out emissions, and suggests that overly lean mixtures created by pilot injections promote CH2O formation when later exposed to high-temperature heat release (HTHR). Injection strategy modulation showed that the absence of HTHR results in minimal CH2O emissions, even when large amount of fuel were injected, emphasizing HTHR’s role in initiating methanol oxidation and CH2O formation. In contrast, strategies promoting lean mixtures followed by HTHR led to higher CH2O emissions due to incomplete oxidations. Additionally, acetaldehyde (CH3CHO) emissions were consistently detected. Chemical kinetic simulations revealed that CH3CHO forms through unimolecular decomposition of EHN-derived intermediates or secondary reactions between methanol and species derived from EHN oxidation like C2H5O2. These results offer new insight into the oxidation behavior of methanol under MCCI conditions and highlight the role of thermal and chemical stratification in pollutant formation.