Land-use/land-cover analysis using Geographic Information System (GIS) application can describe and quantify the transformation of the landscape, evaluating the effectiveness of municipal planning in driving urban expansion. This approach was applied in the municipality of Spongano (Salento, South Italy) in order to evaluate the spatial heterogeneity and the transformations of the land use/land cover from 1988 to 2016. This approach was also used to examine the spread of Xylella fastidiosa, which is a plant pathogen of global importance that is reshaping the Salento landscape. The land-use maps are based on the CORINE Land Cover project classification, while the topological consistency was verified through field surveys. A change detection analysis was carried out using the land-use maps of 1988 and 2016. The most extensive land-use class is olive groves (34–36%), followed by non-irrigated arable lands and shrub and/or herbaceous vegetation associations. The main transition of land involved non-irrigated arable lands, which lost 76 ha and 23 ha to shrub and olive areas, respectively. Meanwhile, the artificial surfaces class doubled its extension, which involved mainly the transition from shrub and heterogeneous agricultural areas. However, the olive groves class is threatened by the dramatic phytosanitary condition of the area, indicating a compromised agroecosystem, which is causing a de facto transition into unproductive areas. The results highlight the inconsistency between what was planned by the urban plan in the past and how the landscape of Spongano has been changed over time. This evidence suggests that it is necessary to develop a plan based on learning by doing, in order to shape and adapt the processes of territorial transformation to the unpredictability of the ecologic, social, and economic systems, as well as ensure that these processes are always focused on environmental issues.