Background: The effects of combining resistance training (RT) and concurrent training (CT; resistance + endurance training) with varied protein doses on bone measures remain poorly understood. Hence, we conducted a comparison of the impacts of two high-protein diets (1.6 or 3.2 g kg−1 d−1) over 16 weeks in resistance-trained males, either with CT or RT alone. Methods: A total of forty-eight males, all of whom were resistance-trained, had the following demographics: 26.6 ± 6 years, body mass index: 25.6 ± 2.9 kg m−2 administered either 3.2 g kg−1 d−1 protein (CT2; n = 12; RT2; n = 12) or 1.6 g kg−1 d−1 protein (CT1; n = 12; RT1; n = 12) during 16 weeks (four sessions·w−1). Bone parameters were assessed pre- and post-intervention. Results: There was no significant interaction between the intervention group and time for the legs, arms, ribs, or pelvis area BMC and BMD (p > 0.05). For the BMD of the pelvis and the BMC of the right ribs, however, there were significant time effects noted (p < 0.05). Furthermore, there was a significant interaction between the intervention group and time in the lumbar and thoracic spines, with a particular time effect noted for the thoracic spine region (p < 0.05). The regional differences in skeletal responses to the intervention are highlighted by these data. Conclusion: Our findings show that the intake of two high-protein diets combined with RT and CT during 16 weeks had no adverse effects on bone tissue parameters. While these findings indicate that protein intake between 2 and 3 times the current RDI does not promote bone demineralization when consumed in conjunction with exercise, future studies investigating the long-term effects of chronic high protein intake on bone tissue health are warranted.