The human microbiome is critical for health across the life course and may mediate the relationship between early-life exposures and health outcomes. The Environmental influences on Child Health Outcomes (ECHO) Cohort provides a unique opportunity to investigate this relationship in children. Individual cohort sites within the ECHO Cohort collected and sequenced microbiome data prior to the consortium formation. Sequencing data were annotated using a common protocol. We summarized the relationship between participant characteristics and features of the microbiome to understand how ECHO can advance the study of the connection between environmental exposures, the microbiome, and health outcomes. A total of 15,509 high-quality extant microbiome samples were collected from 1,086 pregnancies and 5,701 children from 21 ECHO cohort sites. The observed microbial communities were shaped by body site, participant type (pregnant person, child), age, and sample processing. Children lived in 40 states across the United States; high-quality geolocation data were available for more than 60% of children with gut samples. Assay measures, including PFAS, and were available for more than 1,000 children with gut samples. Extant ECHO microbiome data provide an opportunity to characterize the effect of environmental exposures on the developing human microbiome and the role of these exposures in shaping long-term health.