In this study, we explore the supporting role of group support systems (GSS) in organizational workgroups that involve groups of distinct social identities. Intergroup processes become relevant and prevalent in such workgroups and trigger new issues. Anonymity is an important feature of GSS concerning the social influence in such intergroup setting whereby it not only shields individual participants’ identities, but also the corresponding groups’ identities. We report on the results of an experiment consisting of 20 workgroups. Results show that the anonymity feature of GSS reduces subjective uncertainty and conformity, increases minority satisfaction, and improves decision quality. The enforcement of common fate and its impact on social influence are also examined. Our findings provide preliminary indication of the usefulness of GSS in intergroup settings of organizational workgroups.