Body weight and adiposity are determined by the balance between energy intake and energy expenditure. The latter is comprised of three major components including metabolic rate, physical activity and thermogenesis. Thermogenesis is defined as the cellular dissipation of energy via heat production. This process has been extensively characterised in brown adipose tissue, wherein uncoupling protein 1 (UCP1) creates a proton leak across the inner mitochondrial membrane, diverting protons away from ATP synthesis and resulting in heat dissipation. Unlike rodents, sheep do not contain a defined or circumscribed brown fat depot but have dispersed brown adipocytes within traditionally white fat depots. Our work focuses on adult sheep, where we use tissue-specific temperature recordings to characterise thermogenesis. We show that in sheep sternal and retroperitoneal adipose tissue and skeletal muscle are the primary sites of thermogenesis. In skeletal muscle thermogenesis occurs via two mechanisms including mitochondrial uncoupling via UCP3 and futile calcium cycling. Weight loss leads to a compensatory decrease in thermogenesis, which primarily manifests in sternal adipose tissue. In sheep, innate differences in thermogenesis are associated with weight gain. Indeed, reduced post-prandial thermogenesis in either skeletal muscle or retroperitoneal adipose tissue can be associated with increased susceptibility to become obese. Thus, we show that tissue-specific differences in thermogenesis can contribute to long term weight regulation in adult large mammals.