So far, energy planning methods faced several challenges in achieving a proper assessment due to the extreme variability of input conditions. To considerably decrease the computational efforts in achieving solutions, most of the analyses reported in the scientific literature assume constant costs and demand over the entire planning horizon in a typical year. However, results might not be perfectly aligned with real ones because of the incapability of some models to address several aspects like energy demand/production variability, energy and technology costs, efficiency degradation, and use of different energy carriers. This paper proposes a novel methodology that optimises both the long-term planning and short-term scheduling decisions in the management of a multi-energy carries community by means of a Mixed Integer Linear Programming model that also considers the modular design of technologies (e.g., technological devices selection from a discrete set of variants). Such a model has been applied to the case study of a University campus in Italy, whose historical demand data were used for its energy planning with a time horizon of 30 years. Three scenarios have been analysed: (i) the Business As Usual, (ii) the Sector-coupling scenario, and, finally, (iii) the Hydrogen deployment one. The results are obtained under different energy scenarios, showing the effectiveness of the methodology in dealing with multi-investment stages at different planning levels in a reasonable computational time. In particular, they showed that deploying more sustainable technologies would increase the cost of the electricity (between 43%–89%), while reducing other energy carriers’ cost (about 60%) and lowering all energy carriers’ carbon footprint (between 50%–80%). From a long-term perspective, (i) the use of sector-coupling technologies is beneficial from both economic and environmental points of view, and ii) dynamic variations of some parameters can strongly affect the deployment of high-cost technologies to be installed beyond 2030.