Microwave radiometry is a suitable technique to measure atmospheric temperature profiles with high temporal resolution during clear sky and cloudy conditions. In this study, we included cloud models in the inversion algorithm of the microwave radiometer TEMPERA (TEMPErature RAdiometer) to determine the effect of cloud liquid water on the temperature retrievals. The cloud models were built based on measurements of cloud base altitude and integrated liquid water (ILW), all performed at the aerological station (MeteoSwiss) in Payerne (Switzerland). Cloud base altitudes were detected using ceilometer measurements while the ILW was measured by a HATPRO (Humidity And Temperature PROfiler) radiometer. To assess the quality of the TEMPERA retrieval when clouds were considered, the resulting temperature profiles were compared to 2 years of radiosonde measurements. The TEMPERA instrument measures radiation at 12 channels in the frequency range from 51 to 57 GHz, corresponding to the left wing of the oxygen emission line complex. When the full spectral information with all the 12 frequency channels was used, we found a marked improvement in the temperature retrievals after including a cloud model. The chosen cloud model influenced the resulting temperature profile, especially for high clouds and clouds with a large amount of liquid water. Using all 12 channels, however, presented large deviations between different cases, suggesting that additional uncertainties exist in the lower, more transparent channels. Using less spectral information with the higher, more opaque channels only also improved the temperature profiles when clouds where included, but the influence of the chosen cloud model was less important. We conclude that tropospheric temperature profiles can be optimized by considering clouds in the microwave retrieval, and that the choice of the cloud model has a direct impact on the resulting temperature profile.