The past as an analogue for the future is one of the main motivations to use climate models for paleoclimate applications. Assessing possible model limitations in simulating past climate changes can lead to an improved understanding and representation of the response of the climate system to changes in the forcing, setting the basis for more reliable information for the future. In this study, the regional climate model (RCM) COSMO-CLM is used for the investigation of the mid-Holocene (MH, 6000 years ago) European climate, aiming to contribute to the solution of the long-standing debate on the reconstruction of MH summer temperatures for the region, and gaining more insights into the development of appropriate methods for the production of future climate projections. Two physically perturbed ensembles (PPEs) are first built by perturbing model physics and parameter values, consistently over two periods characterized by different forcing (i.e., the MH and pre-industrial, PI). The goal is to uncover possible processes associated with the considered changes that could deliver a response in MH summer temperatures closer to evidence from continental-scale pollen-based reconstructions. None of the investigated changes in model configuration produces remarkable differences with respect to the mean model behavior. This indicates a limited sensitivity of the model to changes in the climate forcing, in terms of its structural uncertainty. Additional sensitivity tests are further conducted for the MH, by perturbing the model initial soil moisture conditions at the beginning of spring. A strong spatial dependency of summer near-surface temperatures on the soil moisture available in spring is evinced from these experiments, with particularly remarkable differences evident over the Balkans and the areas north of the Black Sea. This emphasizes the role of soil–atmosphere interactions as one of the possible drivers of the differences in proxy-based summer temperatures evident between northern and southern Europe. A well-known deficiency of the considered land scheme of COSMO-CLM in properly retaining spring soil moisture, confirmed by the performed tests, suggests that more attention should be paid to the performance of the soil component of climate models applied to this case study. The consideration of more complex soil schemes may be required to help bridging the gap between models and proxy reconstructions. Finally, the distribution of the PPEs with changes in model configuration is analyzed for different variables. In almost all of the considered cases the results show that what is optimal for one period, in terms of a model configuration, is not the best for another characterized by different radiative forcing. These results raise concerns about the usefulness of automatic and objective calibration methods for RCMs, suggesting that a preferable approach is the production of small PPEs that target a set of model configurations, properly representing climate phenomena characteristic of the target region and that will be likely to contain the best model answer under different forcing.