Chronic kidney disease (CKD) is associated with a series of mineral bone disturbances due to increased production of parathormone which increases the activity of osteoclasts, removing calcium and phosphorous from the bones. However, the literature lacks investigations on the feasibility of different resistance training (RT) methods, such as cluster-sets, in this population. Thus, the aim of the present study was to compare traditional versus cluster-set RT protocols on bone mineral density (BMD) T-score, BMD Total, femur BMD, L3-L4 BMD, femoral neck BMD, Klotho, FGF23, Klotho - FGF23 ratio, Sclerostin, vitamin D, phosphorous and calcium in older subjects with CKD. Seventy-eight older subjects (age: 57.55 ± 4.06 years, body mass: 72.26 ± 13.96 kg, body mass index: 26.73 ± 2.97 kg/m2) with CKD undergoing maintenance hemodialysis were randomly divided into control group (CG, n = 26), traditional RT (RT, n = 26) and cluster-set RT (RT-CS, n = 26) groups. Subjects completed 24 weeks of RT three times per week, 1 h and 30 min before the hemodialysis session, and each training lasted around 60 to 80 min. There was a group×time interaction for total BMD, femur BMD, L3-L4 BMD, and femoral neck BMD, revealed by improvements for RT and RT-CS groups (pre versus post). Only femur BMD displayed differences as compared with the CG. Minimum clinically important difference (MCID) values revealed more responsive subjects in the RT-CS group for total BMD, femur BMD, klotho, FGF23, sclerostin, Vitamin D and calcium. In conclusion, RT can be used as a non-pharmacological complementary strategy for the treatment of CKD. RT-CS may be useful for these subjects as more responders were found for this type of training.