This multi-method longitudinal study sought to investigate linkage in parental neuroendocrine functioning – indicated by cortisol – over two measurement occasions. In addition, we examined how parental cortisol linkage may operate as an intermediate factor in the cascade of contextual risks and parenting. Participants were 235 families with a young child (Mage = 33.56, 36.00 years for mothers and fathers respectively), who were followed for two annual measurement occasions. Parental cortisol linkage was measured around a laboratory conflict discussion task at both measurement occasions (i.e., pre-discussion, 20- and 40-minute post-discussion for each measurement occasion). Maternal and paternal parenting behavior was observed during a parent-child discipline discussion task. Findings indicated similar levels of cortisol linkage between parents over the two measurement occasions. Furthermore, cortisol linkage between parents operated as an intermediate factor between contextual risks and more compromised parenting behavior. That is, greater contextual risks, indicated by greater neighborhood risk and interparental conflict, were linked to greater cortisol linkage between parents over time, which was in turn linked to greater authoritarian parenting during parent-child interaction. Findings highlighted the importance of understanding physiological-linkage processes with respect to the impact of contextual risks on family functioning and may have crucial implications for clinical work.