Joint performance can lead to the synchronization of physiological processes among group members during a shared task. Recently, it has been shown that synchronization is indicative of subjective ratings of group processes and task performance. However, different methods have been used to quantify synchronization, and little is known about the effects of the choice of method and level of analysis (individuals, dyads, or triads) on the results. In this study, participants performed a decision‐making task in groups of three while physiological signals (heart rate and electrodermal activity), positive affective behavior, and personality traits were measured. First, we investigated the effects of different levels of analysis of physiological synchrony on affective behavior. We computed synchrony measures as (a) individual contributions to group synchrony, (b) the average dyadic synchrony within a group, and (c) group‐level synchrony. Second, we assessed the association between physiological synchrony and positive affective behavior. Third, we investigated the moderating effects of trait anxiety and social phobia on behavior. We discovered that the effects of physiological synchrony on positive affective behavior were particularly strong at the group level but nonsignificant at the individual and dyadic levels. Moreover, we found that heart rate and electrodermal synchronization showed opposite effects on group members' display of affective behavior. Finally, trait anxiety moderated the relationship between physiological synchrony and affective behavior, perhaps due to social uncertainty, while social phobia did not have a moderating effect. We discuss these results regarding the role of different physiological signals and task demands during joint action.