This study introduces and tests the MAGUS (Model for the Analysis of Geomorphological Urban Systems), a GIS-based methodological framework designed to analyze the complex interplay between urbanization and natural landscapes. Focusing on the historical evolution of Turin city center (Italy), the research employs an interdisciplinary approach to examine how urban expansion has interacted with pre-existing geomorphological features. The study leverages historical documents, digitized and georeferenced within a cartographic space, to reveal the relationships between natural and anthropogenic landforms from the Roman period through the 20th century. A key innovation of MAGUS is the integration of Multi-Temporal Markers (MTM) and Volumetric Unit of Building (VUB), which enhances the accuracy of historical data analysis. The results demonstrate that urbanization significantly alters the natural landscape in the historic city center of Turin, where the stratification of urban expansion phases partially obscures the original landform. By overlaying topographical data with historical urban expansion maps, the research highlights the concealed geomorphological elements beneath Turin’s urban fabric. This interdisciplinary study not only contributes to the field of urban geomorphology but also provides a foundation for future research into the impacts of urbanization on natural landscapes, which is increasingly critical as urban populations continue to grow.