Low-protein and high-protein diets regulate energy metabolism in animals and humans. To evaluate whether different dietary protein sources modulate energy balance when ingested at average levels obesity-prone male C57BL/6J mice were pair-fed high-fat diets (67 energy percent fat, 18 energy percent sucrose and 15 energy percent protein) with either casein, chicken filet or a mixture of cod and scallop (1:1 on amino acid content) as protein sources. At equal energy intake, casein and cod/scallop fed mice had lower feed efficiency than chicken fed mice, which translated into reduced adipose tissue masses after seven weeks of feeding. Chicken fed mice had elevated hepatic triglyceride relative to casein and cod/scallop fed mice and elevated 4 h fasted plasma cholesterol concentrations compared to low-fat and casein fed mice. In casein fed mice the reduced adiposity was likely related to the observed three percent lower apparent fat digestibility compared to low-fat, chicken and cod/scallop fed mice. After six weeks of feeding an oral glucose tolerance test revealed that despite their lean phenotype, casein fed mice had reduced glucose tolerance compared to low-fat, chicken and cod/scallop fed mice. In a separate set of mice, effects on metabolism were evaluated by indirect calorimetry before onset of diet-induced obesity. Spontaneous locomotor activity decreased in casein and chicken fed mice when shifting from low-fat to high-fat diets, but cod/scallop feeding tended (P = 0.06) to attenuate this decrease. Moreover, at this shift, energy expenditure decreased in all groups, but was decreased to a greater extent in casein fed than in cod/scallop fed mice, indicating that protein sources regulated energy expenditure differently. In conclusion, protein from different sources modulates energy balance in C57BL/6J mice when given at normal levels. Ingestion of a cod/scallop-mixture prevented diet-induced obesity compared to intake of chicken filet and preserved glucose tolerance compared to casein intake.