The airborne prism experiment (APEX) is an imaging spectrometer developed by a joint Swiss–Belgian consortium composed of institutes (University of Zurich, Flemish Institute for Technological Research) and industries (RUAG, OIP, Netcetera), supported by the European Space Agency’s PRODEX programme. APEX is designed to support the development of future space-borne Earth observation systems by simulating, calibrating or validating existing or planned optical satellite missions. Therefore, periodic extensive calibration of APEX is one major objective within the project. APEX calibration under laboratory conditions is done at its dedicated calibration and characterization facility at the German Aerospace Center (DLR) in Oberpfaffenhofen, Germany. While environmental influences under laboratory conditions are reduced to a minimum, the effects of atmospheric absorption and the properties of the underlying calibration infrastructure may still influence the measurements and subsequently the accuracy of the sensor spectral response estimations. It is demonstrated that even a lightpath of ∼2 m through the atmosphere or the monochromator grating can have significant impact on the spectral response estimation of the sensor. A normalization approach described in this letter is able to compensate for these effects. The correction algorithm is exemplarily demonstrated on actual measurements for the short wavelength-IR range channel.