Since approximately 75% of Europeans currently live in cities, and this number will rise, urban areas are the most important testbeds for energy transition, climate change adaptation measures, and decarbonisation models, on which studies and efforts for concrete change must focus. The teaching of mitigation and adaptation measures to climate change and decarbonisation models has gradually taken up space within university courses. However, the complexity of the decarbonisation issue is raising awareness on the urgency of an interdisciplinary approach that can be conveyed by spatial planning. Currently, this approach is not widespread in Higher Education Institutions in Europe but is nonetheless necessary to let new professional profiles emerge who are able to coordinate different stakeholders, data, and information sources. The Erasmus+ project CITY MINDED (2020–2022) has worked in this direction, by developing and testing a methodology for the design of a structured ordinary practice for teaching urban decarbonisation to students in Higher Education. This practice (at the same time, interdisciplinary, collaborative, experiential, and place-based) aims to offer students a combination of different approaches and working methods to investigate and improve urban neighbourhoods and districts, resulting in the definition of an operative roadmap for decarbonisation in the medium-to-long-term. The aim of this article is to highlight the learning-by-doing experience developed by the project consortium, with reference to the testing of the methodology conducted within an Intensive Course in the City of Valletta (Malta). In particular, the paper illustrates how this experience succeeded in stimulating students with different academic backgrounds to establish connections across disciplines, in raising their awareness about the complexity of city decarbonisation processes. Overcoming the strict time and budget constraints of an EU-funded project, such an approach can be further developed, replicated on theoretical grounds, and implemented within different degree programmes dealing with urban sustainability.