A modified form of the sequential function specification method (SFSM) is developed with specific consideration given to multiple time scales in an effort to avoid overregularization of the solution estimates. The authors extend their approach to solve the inverse heat conduction problem (IHCP) associated with the application of thermal barrier coatings (TBC) to in-cylinder surfaces of an internal combustion engine. Subsurface temperature measurements are used to calculate surface heat flux profiles. The modified inverse solver is validated ex situ using a custom fabricated radiation chamber. The solution methodology is extended in situ to evaluate temperature data collected from a single-cylinder research engine operating in homogeneous charge compression ignition (HCCI) mode. Crank angle resolved, thermal barrier coating surface temperature and heat flux profiles are produced—enabling correlation of thermal conditions at the gas-wall boundary with engine performance, emission, and efficiency metrics.