The second millennium BC was a period of significant social and environmental changes in prehistoric India. After the disintegration of the Indus civilization, in a phase known as the Early Jorwe (1400–1000 BC), hundreds of agrarian villages flourished in the Deccan region of west‐central India. Environmental degradation, combined with unsustainable agricultural practices, contributed to the abandonment of many communities around 1000 BC. Inamgaon was one of a handful of villages to persist into the Late Jorwe phase (1000–700 BC), wherein reliance on dry‐plough agricultural production declined. Previous research demonstrated a significant decline in body size (stature and body mass index) through time, which is often used to infer increased levels of biocultural stress in bioarchaeology. This article assesses evidence for growth disruption in the immature human skeletal remains from Inamgaon by correlating measures of whole bone morphology with midshaft femur compact bone geometry and histology. Growth derangement is observable in immature archaeological femora as an alteration in the expected amount and distribution of bone mass and porosity in the midshaft cross‐section. Cross‐section shape matched expectations for older infants with the acquisition of bipedal locomotion. These results support the hypothesis that small body size was related to disruptions in homeostasis and high levels of biocultural stress in the Late Jorwe at Inamgaon. Further, the combined use of geometric properties and histological details provides a method for teasing apart the complex interactions among activity and “health,” demonstrating how biocultural stressors affect the acquisition and quality of bone mass. Am J Phys Anthropol :1–17, 2014. © 2014 Wiley Periodicals, Inc.