In August 2018, the European Space Agency (ESA) launched the first Doppler wind lidar into space, which has since then been providing continuous profiles of the horizontal line-of-sight wind component at a global scale. Aeolus data have been successfully assimilated into several numerical weather prediction (NWP) models and demonstrated a positive impact on the quality of the weather forecasts. To provide valuable input data for NWP models, a detailed characterization of the Aeolus instrumental performance as well as the realization and minimization of systematic error sources is crucial. In this paper, Aeolus interferometer spectral drifts and their potential as systematic error sources for the aerosol and wind products are investigated by means of instrument spectral registration (ISR) measurements that are performed on a weekly basis. During these measurements, the laser frequency is scanned over a range of 11 GHz in steps of 25 MHz and thus spectrally resolves the transmission curves of the Fizeau interferometer and the Fabry–Pérot interferometers (FPIs) used in Aeolus. Mathematical model functions are derived to analyze the measured transmission curves by means of non-linear fit procedures. The obtained fit parameters are used to draw conclusions about the Aeolus instrumental alignment and potentially ongoing drifts. The introduced instrumental functions and analysis tools may also be applied for upcoming missions using similar spectrometers as for instance EarthCARE (ESA), which is based on the Aeolus FPI design.