Objectives Anthropological studies of cortical bone often aim to reconstruct either habitual activities or health of past populations. During development, mechanical loading and metabolism simultaneously shape cortical bone structure; yet, few studies have investigated how these factors interact. Understanding their relative morphological effects is essential for assessing human behavior from skeletal samples, as previous studies have suggested that interaction effects may influence the interpretation from cortical structure of physical activity or metabolic status. Material and Methods This study assesses cross‐sectional geometric and histomorphometric features in bones under different loading regimes (femur, humerus, rib) and compares these properties among individuals under different degrees of metabolic stress. The study sample consists of immature humans from a late medieval Lithuanian cemetery (Alytus, 14th–18th centuries AD). Analyses are based on the hypothesis that metabolic bone loss is distributed within the skeleton in a way that optimizes mechanical competency. Results Results suggest mechanical compensation for metabolic bone loss in the cross‐sectional properties of all three bones (especially ribs), suggesting a mechanism for conserving adequate bone strength for different loads across the skeleton. Microscopic bone loss is restricted to stronger bones under high loads, which may mitigate fracture risk in areas of the skeleton that are more resistive to loading, although alternative explanations are examined. Discussion Distributions of metabolic bone loss and subsequent structural adjustments appear to preserve strength. Nevertheless, both mechanics and metabolism have a detectable influence on morphology, and potential implications for behavioral interpretations in bioculturally stressed samples due to this interaction are explored. Am J Phys Anthropol 160:317–333, 2016. © 2016 Wiley Periodicals, Inc.