Interpersonal physiological synchrony refers to the temporal coordination of autonomic states during social encounters. Previous studies indicate that physiological synchrony may arise during nonverbal interactions. Nevertheless, the role played by contextual and individual factors in determining its emergence is understudied. In this work, we examined heart rate synchrony during a cooperative joint action task, exploring how task constraints, novelty, and behavioral synchrony influence physiological alignment. To achieve this, we periodically modulated task demands by alternating between peer-to-peer and leader–follower dynamics, as well as between complementary and imitative movements, and their combinations. Additionally, we assessed the role of individual differences by examining the impact of dyad members' Social Anxiety and Perspective Taking levels. We further investigated how task demands and personal traits shape the perceived quality of social interactions and subject-level heart rate variability. Our findings revealed a significant increase in physiological synchrony and a decrease in perceived interaction quality when participants switched to a novel task version (i.e., during switch blocks) compared to task repetition. Task switching was also associated with increased heart rate variability. Notably, Social Anxiety negatively predicted physiological synchrony, suggesting that more socially anxious dyads were less likely to achieve physiological alignment. However, no relationship was observed between physiological synchrony and task performance. Overall, our results suggest that physiological synchrony intensifies when dyads navigate the challenge of learning a novel task together, and that both contextual and individual aspects contribute to its emergence.