Background: Little is known about the effect of exercise modality during a dietary weight loss program on muscle size and quality, as measured by computed tomography (CT). Even less is known about how CT-derived changes in muscle track with changes in volumetric bone mineral density (vBMD) and bone strength. Methods: Older adults (66 ± 5 years, 64 % women) were randomized to 18-months of diet-induced weight loss (WL), WL with aerobic training (WL + AT), or WL with resistance training (WL + RT). CT-derived muscle area, radio-attenuation and intermuscular fat percentage at the trunk and mid-thigh were determined at baseline (n = 55) and 18-month follow-up (n = 22–34), and changes were adjusted for sex, baseline value, and weight lost. Lumbar spine and hip vBMD and finite element-derived bone strength were also measured. Results: After adjustment for the weight lost, muscle area losses at the trunk were −7.82 cm2 [−12.30, −3.35] for WL, −7.72 cm2 [−11.36, −4.07] for WL + AT, and −5.14 cm2 [−8.65, −1.63] for WL + RT (p