This study examined how temporal associations between parents’ physiological and behavioral responses may reflect underlying regulatory difficulties in at-risk parenting. Time-series data of cardiac indices (second-by-second estimates of inter-beat intervals – IBI, and respiratory sinus arrhythmia – RSA) and parenting behaviors were obtained from 204 child welfare-involved parents (88% mothers, Mage = 32.32 years) during child-led play with their 3- to 7-year-old children (45.1% female; Mage = 4.76 years). Known risk factors for maltreatment, including parents’ negative social cognitions, mental health symptoms, and inhibitory control problems, were examined as moderators of intra-individual physiology-behavior associations. Results of ordinary differential equations suggested increases in parents’ cardiac arousal at moments when they showed positive parenting behaviors. In turn, higher arousal was associated with momentary decreases in both positive and negative parenting behaviors. Individual differences in these dynamic processes were identified in association with parental risk factors. In contrast, no sample-wide RSA-behavior associations were evident, but a pattern of increased positive parenting at moments of parasympathetic withdrawal emerged among parents showing more total positive parenting behaviors. This study illustrated an innovative and ecologically-valid approach to examining regulatory patterns that may shape parenting in real-time and identified mechanisms that should be addressed in interventions.