According to the latest energy efficiency European directive (EED 2023/1791/EU), the expected energy renovation rate of at least 3% of the buildings’ floor area each year towards nearly zero-energy buildings (nZEBs) is extended to include public buildings not only of the central government (as per the first EED 2012/27/EU) but also of regional and local authorities. This poses a great challenge, especially for Municipalities that often manage large building stocks with high energy demands. In response to this challenge, this paper presents the application of the so-called “typology approach” for conducting public buildings’ energy renovation plans at the local level. A computational survey is initially introduced to decide the optimal set of building-stock clustering criteria among all possible combinations, involving the minimization of the RMSE index regarding the primary energy consumption of each building. For a representative building from each identified typology, the key performance indicators (KPIs) are computed for alternative energy-upgrading scenarios. Exploiting the IMPULSE Interreg-MED project tools, the KPIs from each representative building are at first extrapolated to all buildings of the examined stock and, finally, a gradual energy renovation plan is automatically produced based on user-defined decision parameters including the required annual renovation rate. The methodology is applied for the case of the Municipality of Hersonissos in Greece. For the specific 44-buildings’ stock it was found that the optimal clustering set included four criteria, building use, construction year, heating, and a cooling system, leading to 15 building typologies. Finally, assuming a 7% renovation rate per year, a 12-year gradual renovation (nZEB transformation) plan is obtained foreseeing an 85% CO₂ emissions’ reduction.