In the present study, we compare energy transition scenarios from a new set of Integrated Assessment Models, the suite of MEDEAS models, based on a systems dynamic modelling approach, with scenarios from two already well know structurally and conceptually different Integrated Assessment Models, the Integrated MARKAL-EFOM System (TIMES) and the Long-range Energy Alternatives Planning system (LEAP). The investigation was carried out to cross-compare and benchmark the response of MEDEAS models with TIMES and LEAP in depicting the energy transition in two different countries, Austria and Bulgaria. The preliminary results show a good agreement across all the models in representing scenarios projecting historical trends, while a major discrepancy is detectable when the rate of implementation of renewable energy is forced to increase to achieve energy system decarbonization. The discrepancy is mainly traceable to the differences in the models’ conception and structures rather than in a real mismatch in representing the same scenarios. The present study is put forward as a guideline for validating new modelling approaches that link energy policy decision tools to the global biophysical and socioeconomic constraints.