Purpose The purpose of this study is to map the intellectual structure of the research concerning conflict and conflict management in virtual teams (VT), to contribute to the further integration of knowledge among different streams of research and to develop an interpretative framework to stimulate future research. Design/methodology/approach A data set of 107 relevant papers on the topic was retrieved using the Web of Science Core Collection database covering a period ranging from 2001 to 2019. A comparative bibliometric analysis consisting of the integration of results from the citation, co-citation and bibliographic coupling was performed to identify the most influential papers. The systematic literature review complemented the bibliometric results by clustering the most influential papers. Findings The results revealed different intellectual structures across several types of analyses. Despite such differences, 41 papers resulted as the most impactful and provided evidence of the emergence of five thematic clusters: trust, performance, cultural diversity, knowledge management and team management. Research limitations/implications Based on the bibliometric analyses an interpretative research agenda has been developed that unveils the main future research avenues. The paper also offers important theoretical contributions by systematizing knowledge on conflict in identifying VTs. Managerial contributions in the form of the identification of best practices are also developed to guide conflict management in VTs. Originality/value The uniqueness of this paper is related to its effort in studying, mapping and systematizing the knowledge concerning the topic of handling conflicts in VTs. Considering the current contingencies, this research is particularly timely.