Within a relationship, stress might be shared and co-regulated between the partners at the physiological level, through cortisol linkage. Cortisol is sensitive to social inputs, and cortisol linkage may reflect stress-related dynamics in a couple or positive relational processes, such as marital distress or shared moments. For many couples, the transition to parenthood is accompanied by acute or chronic stressors that can impact the relationship. Concurrently, having a supportive and responsive partner becomes an important resource to adapt to the manifold changes. These relational processes may also play a role with respect to cortisol linkage. The current article reports a study that examined changes of cortisol linkage across the transition to parenthood, and whether high levels of psychological stress and perceived partner responsiveness were associated with stronger cortisol linkage. We used data from a longitudinal study of 120 couples (N = 240) who transitioned to parenthood. Participants collected saliva samples and completed an ecological momentary assessment over three consecutive days, during pregnancy, at 6 months and at 18 months postpartum. Cortisol linkage among partners was significant and positive, increased in strength from pregnancy to 6 months postpartum, and remained stable from 6 months to 18 months postpartum. Within-couples, higher levels of psychological stress were associated with a stronger linkage between partners, while higher perceived partner responsiveness was associated with a weaker cortisol linkage. These findings provide further evidence of cortisol linkage during the transition to parenthood, and its associations with positive and negative relational processes.