Parent–child relationship dynamics have been shown to predict socioemotional and behavioral outcomes for children, but little is known about how they may affect biological development. The aim of this study was to test if observational assessments of parent–child relationship dynamics (cohesion, enmeshment, and disengagement) were associated with three biological indices of early life adversity and downstream health risk: (1) methylation of the glucocorticoid receptor gene (NR3C1), (2) telomere attrition, and (3) mitochondrial biogenesis, indexed by mitochondrial deoxyribonucleic acid (DNA) copy number (mtDNAcn), all of which were measured in children's saliva. We tested hypotheses using a sample of 254 preschool‐aged children (M age = 51.04 months) with and without child welfare‐substantiated maltreatment (52% with documented case of moderate‐severe maltreatment) who were racially and ethnically diverse (17% Black, 40% White, 23% biracial, and 20% other races; 45% Hispanic) and from primarily low‐income backgrounds (91% qualified for public assistance). Results of path analyses revealed that: (1) higher parent–child cohesion was associated with lower levels of methylation of NR3C1 exon 1D and longer telomeres, and (2) higher parent–child disengagement was associated with higher levels of methylation of NR3C1 exon 1D and shorter telomeres. Results suggest that parent–child relationship dynamics may have distinct biological effects on children.