β-conglycinin (β-Con) is one of the major proteins in soy protein (SP), and intake of β-Con can be expected to yield various health benefits, including the induction of beige adipocyte formation. However, it is not practical for most people to satisfy their dietary protein requirements with SP alone. In addition, combining exercise with at least partial replacement of dietary protein with SP might synergistically yield various health benefits. In this study, we found that a 50β-Con diet (10.6 g β-Con and 0.37 g methionine/100 g diet) in combination with exercise for 4 weeks synergistically induced the formation of beige adipocytes, unlike 50β-Con or exercise alone. Furthermore, the unique inductive effect was associated with the activation of transcription factor 4− fibroblast growth factor 21 signaling. The combination of exercise with protein intake partially replaced with β-Con may provide various health benefits, including beige adipocyte formation.