The loss and fragmentation of habitats caused by anthropogenic activities in the last decades has affected foraging habitat quality and, therefore, foraging success (food quantity, quality and foraging range) of many animals, including many pollinators. Honeybees (Apis mellifera) are important pollinators of many plant species, and habitat change has also affected their ability to collect the resources they need to maintain the colony. Two important biological traits that might be affected by land use are body size and fat stores, which have the potential to affect body condition, and therefore success, and colony health. However, few studies have investigated these traits in different landscapes and different times of year. We surveyed 47 sites in three different landscape types (agriculture, urban and mixed habitats) in south-western Germany. We measured honeybee body size, wing wear and analysed body fat quantity and composition using GC-MS in the spring, summer and autumn. We found that summer honeybees were smaller in urban and mixed habitats, they showed the greatest wing wear, but they had 18.4-21.3% larger fat stores compared to agricultural sites. Bees in agricultural habitats experienced a drop in fat stores in summer, while body size remained unaffected. In autumn, just before honeybees enter the inactive winter period, bees in urban and mixed areas experienced a drop in fat stores. Wing length decreased from spring to autumn irrespective of habitat type. Our findings indicate that bees in agricultural settings experience physiological challenges in a central European region in summer, possibly because urban and mixed habitats provide better nutritional conditions during summer. Our findings, thus, confirm that honeybees undergo morphological and physiological changes in response to land use and season, which could impact their physiological condition and winter survival.