Clean and efficient internal combustion engine performance will play a significant role in the move to a decarbonized energy system. Currently, fuel deposit formation on engine components negatively impacts CO2 and pollutant emissions, where previous attempts at deposit characterization afforded non-diagnostic chemical assignments. Here, we uncover the identity and 3D spatial distribution of molecular species from gasoline, diesel injector and filter deposits with the 3D OrbiSIMS technique. Alkylbenzyl sulfonates, derived from lubricant oil contamination in the engine fuel cycle, were common to samples, we evidence transformation of the native sulfonate to longer chain species by reaction with fuel fragments in the gasoline deposit. Inorganic salts, identified in both diesel deposits, were prevalent throughout the injector deposits depth. We identified common polycyclic aromatic hydrocarbons up to C66H20, these were prevalent in the gasoline deposits lower depths. This work will enable deposit mitigation by unravelling their chemical composition, spatial distribution, and origins.