Developmental plasticity models hypothesize the role of genetic and prenatal environmental influences of the development of the hypothalamic-pituitary-adrenal (HPA) axis and highlight the potential for the organizational influences of genes and the prenatal environment to moderate early postnatal environmental influences on HPA functioning. This article examines the interplay of genetic, prenatal, and parenting influences across the first 4.5 years of life on a novel index of children’s HPA flexibility at 4.5 years of age using repeated measures of cortisol across three days. Data were obtained from 210 adoption-linked families, adopted children and both their adoptive parents and birth mothers, who participated in a longitudinal, prospective US domestic adoption study. Genetic and prenatal influences moderated associations between within-person changes in over-reactive parenting influences from 9 months to 4.5 years of age and children’s HPA flexibility at age 4.5 years in different ways for mothers and fathers’ parenting. Findings supported developmental plasticity models and uncovered novel developmental, gene X environment, and prenatal X environment influences on children’s cortisol functioning.