Cortisol, a key biomarker of hypothalamus–pituitary–adrenal (HPA) axis activity, is central to early stress regulation and neurodevelopment. While prior studies have linked maternal and infant cortisol to child outcomes, less is known about their synchrony during early infancy, a time of rapid neuroendocrine development. In this longitudinal study, we examined cortisol coupling and the correlation with maternal adverse childhood experiences (ACEs) in 305 mother–infant dyads from São Paulo, Brazil. Salivary cortisol was collected at ~ 1 month (32.3 days) and 6 months postpartum. We assessed intra- and interindividual cortisol dynamics and coupling using bivariate latent change score modeling. Maternal and infant cortisol were positively correlated at baseline (r = 0.319, p < 0.001) and at 6 months (r = 0.208, p = 0.003), suggesting early attunement that diminishes over time. Mothers and infants showed negative self-feedback, where higher baseline cortisol predicted smaller changes (mothers: B = -0.654; infants: B = -0.615; both p < 0.001). Maternal ACEs predicted elevated maternal cortisol at baseline (B = 0.126, p = 0.026) but did not affect the rate of change. These findings reveal early HPA synchrony and gradual decoupling, and highlight the lasting effects of maternal adversity on postpartum stress physiology.