Recent studies have demonstrated the efficacy of integrating diverse fields such as archaeology, isotope geochemistry, oral biology, and public health for understanding ancient human biology. Here we document the early lives of five individuals from Pain Haka, a large open-air Neolithic burial site on the island of Flores, Indonesia dating to 2200 to 3000 years BP. We characterize microscopic tooth development and developmental stress histologically, followed by documentation of trace element concentrations and oxygen isotope values via two cutting-edge mass spectrometry techniques. Molar formation times are similar to contemporary modern human populations. All individuals show pronounced non-specific stress indicators (internal accentuated lines) during the first few years of life. Nursing behaviour revealed from calcium-normalized barium distributions appears to have varied considerably, ranging from one individual that likely ceased breastfeeding prior to nine months of age to another who may have nursed for three or more years. In the former instance, this individual shows major developmental disruptions and possible skeletal remineralization during the second year of life. This was inferred from accentuated lines that were structurally discontinuous and coincident discrete bands of calcium-normalized barium after milk input had ceased. All five individuals showed some degree of lead exposure during their childhoods. Fine-scale (nearly weekly) oxygen isotope values reveal annual precipitation cycles in the majority of individuals, with δ18O values that are similar to those of contemporary Australasian humans and large-bodied Indonesian primates. This interdisciplinary approach reveals patterns of ancient human diet, health, and environmental variation with unprecedented detail. This project is funded by the Australian Academy of Science Regional Collaborations Program, the Australian Research Council, and the U.S. National Institutes of Health.