A HVAC controller includes a housing and one or more heat-generating components contained within the housing. The heat-generating components cause a temperature inside the housing to exceed a temperature outside the housing. The controller includes a temperature sensor configured to measure the temperature inside the housing and a controller event detector configured to detect, for each of the heat-generating components, a controller event that generates heat inside the housing. The controller further includes a temperature compensation module configured to identify a steady-state temperature gain associated with each of the detected controller events, to calculate a temperature offset using a summation of the steady-state temperature gains, and to determine the temperature of the building zone outside the housing by subtracting the temperature offset from the temperature measured inside the housing.