Many factors negatively affect domesticated honeybee (Apis mellifera) health, causing a global decrease in their population year after year with major losses occurring during winter, and the cause remains unknown. Here, we monitored for 12 months North American colonies of honeybees enduring important temperature variations throughout the year, to assess the metabolism and immune system of summer and winter honeybee individuals. Our results show that in flight muscle, mitochondrial respiration via complex I during winter is drastically reduced compared with summer. However, the capacity for succinate and glycerol-3-phosphate (G3P) oxidation by mitochondria is increased during winter, resulting in higher mitochondrial oxygen consumption when complex I substrates, succinate and G3P were assessed altogether. Pyruvate kinase, lactate dehydrogenase, aspartate aminotransferase, citrate synthase and malate dehydrogenase tend to have reduced activity levels in winter, unlike hexokinase, NADH dehydrogenase and pyruvate dehydrogenase. Transcript abundance of highly important immunity proteins such as Vitellogenin and Defensin-1 were also increased in winter bees, and a stronger phagocytic response as well as a better hemocyte viability was observed during winter. Thus, a reorganization of substrate utilization favoring succinate and G3P while negatively affecting complex I of the ETS is occurring during winter. We suggest that this might be due to complex I transitioning to a dormant conformation through post-translational modification. Winter bees also have an increased response for antibacterial elimination. Overall, this study highlights previously unknown cellular mechanisms between summer and winter honeybees that further our knowledge about this important species.