Individuals with lower-limb amputations, many of whom have type 2 diabetes, experience impaired musculoskeletal health. This study: (1) compared residual and intact limbs of diabetic and non-diabetic post-mortem individuals with amputation to identify structures vulnerable to injury, and (2) compared findings to diabetic and healthy control groups to differentiate influences of amputation and diabetes on musculoskeletal health. Postmortem CT scans of three groups, ten individuals each, were included: (1) individuals with transtibial or transfemoral amputations, half with diabetes (2) diabetic controls, and (3) healthy controls. Hip and knee joint spaces, cross-sectional thigh muscle and fat areas, and cross-sectional bone properties (e.g. area, thickness, geometry) were measured. Wilcoxon Signed-Rank and Kruskal–Wallis tests assessed statistical significance. Asymmetry percentages between limbs assessed clinical significance. Residual limbs of individuals with amputation, particularly those with diabetes, had significantly less thigh muscle area and thinner distal femoral cortical bone compared to intact limbs. Compared to control groups, individuals with amputation had significantly narrower joint spaces, less thigh muscle area bilaterally, and thinner proximal femoral cortical bone in the residual limb. Diabetic individuals with amputation had the most clinically significant asymmetry. Findings tended to align with those of living individuals. However, lack of available medical information and small sample sizes reduced the anticipated clinical utility. Larger sample sizes of living individuals are needed to assess generalizability of findings. Quantifying musculoskeletal properties and differentiating influences of amputation and diabetes could eventually help direct rehabilitation techniques.