Semivolatile organic compounds (SVOCs) are widely detected in many indoor environments due to their frequent use in building materials, textiles, furniture, electronics, and other consumer products. Biomarkers of SVOC exposures have been consistently measured in biological samples across the globe, presenting uncertainty about their potential impacts on sensitive populations. To begin unravelling the dynamics between gut microbiome maturation and chronic exposure to complex chemical mixtures, this study characterized the prokaryotic and fungal gut microbiomes of children (ages 3-6) in a North Carolina cohort and examined their relationships with SVOC exposures. SVOC biomarkers were detected ubiquitously in pooled urine samples, with 29 compounds detected in >95% of samples. In total, 61 bacterial taxon-biomarker and 24 fungal taxon-biomarker pairs displayed statistically significant relationships (i.e., minimum positive rs ≥ 0.2 or minimum negative rs ≤ -0.2; p < 0.05), with disparate trends noted for bacteria and fungi. Sm-PFOS was associated with declines in several bacterial taxa (rs ≤ -0.21; p ≤ 0.05), while phthalate metabolites like MHiBP were negatively associated with fungi (rs ≤ -0.45). Finally, 10 genera historically capable of reductive dehalogenation displayed significant positive associations with halogenated SVOCs (e.g., biomarkes of chlorobenzenes such as 2,4-DCP), suggesting these compounds may act as a selective pressure within developing gut microbiomes.