The European ground squirrel (Spermophilus citellus, EGS), IUCN EN, population decline is of great ecological concern, threatening to destabilize remnant grassland areas. The differences in characteristics of EGS occupied and unoccupied areas within grassland habitats are elusive. There is an urgent need to assess subtle changes in grassland cover properties within the available habitat at higher spatial and temporal resolutions. Here, we inspected and characterized species’ habitat properties by using object-based image classification (OBIA) of high-resolution (HR) images acquired from an unmanned aerial vehicle (UAV). Image segmentation and classification processes were performed by open-source Orfeo ToolBox (OTB) in the QGIS software. We determined the land cover classes and their characteristics within the species’ habitat occupied area and its surroundings. These results improve data sets for criteria-based analysis of EGS habitat suitability. The study evidence how data derived from new tools provides a different perspective to the endangered species habitat assessment.