This study took a multi-analytical approach including group differences, correlations and unit-weighed directional z-score comparisons to identify the key mediators of bone health. A total of 190 participants (18–80 years) were categorized by body fat%, body mass index (BMI) and fat mass index (FMI) to examine the effect of differing obesity criteria on bone characteristics. A subset of 50 healthy-eating middle-to-older aged adults (44–80 years) was randomly selected to examine any added impact of lifestyle and inflammatory profiles. Diet was assessed using a 3-day food diary, bone mineral density (BMD) and content (BMC) by dual energy x-ray absorptiometry in the lumbar, thoracic, (upper and lower) appendicular and pelvic areas. Physical activity was assessed using the Baecke questionnaire, and endocrine profiling was assessed using multiplex luminometry. Obesity, classed via BMI, positively affected 20 out of 22 BMC- and BMD-related outcome measures, whereas FMI was associated with 14 outcome measures and adiposity only modulated nine out of 22 BMC- and BMD-related outcome measures. Whilst bivariate correlations only linked vitamin A and relative protein intake with BMD, the Z-score composite description presented a significantly different overall dietary quality between healthy and osteopenic individuals. In addition, bivariate correlations from the subset revealed daily energy intake, sport-based physical activity and BMI positive mediators of seven out of 10 BMD sites with age and body fat% shown to be negative mediators of bone characteristics. In conclusion, whilst BMI is a good indicator of bone characteristics, high body fat% should also be the focus of osteoporosis risk with ageing. Interestingly, high BMI in conjunction with moderate to vigorous activity supplemented with an optimal diet (quality and quantity) are identified as positive modulators of bone heath.