We analyzed variation in the distribution of eastern Hermann's tortoise (Testudo hermanni boettgeri) in a complex landscape consisting of both natural and human-altered habitats in a temperate climate region in Serbia. Our results indicated nonrandom distribution of tortoises within different habitat types with large and medium effect size for year and activity pattern, respectively. Additionally, the tortoises expressed relatively weak preference for habitats modified by human activity (e.g., vineyards, orchards, or gardens). The results suggested that these tortoises preferred some particular habitats more than others when performing specific activities. They also did not exhibit the same distribution pattern among habitats over consequent years. In other words, they were not randomly distributed among habitat types with regard to specific activity or year. The information on preferences in complex habitat systems is important for the conservation management of eastern Hermann's tortoise and should be considered when planning activities related to sustainable development within the region of study.