This case study was conducted in two high school classrooms that utilized collaborative project-based learning (PBL). Collaboration is an important instructional strategy, especially used in conjunction with PBL, and is an essential learning outcome for the twenty-first century. This study examined how collaboration can be achieved as a learning outcome and used effectively as an instructional method by understanding what causes task-, process-, and relationship-related intragroup conflict and how social skills are related to intragroup conflict and collaboration at both the individual and group levels. Literature suggests that, while task-related conflict serves as a catalyst for collaboration, process- and relationship-related conflicts are detrimental to collaboration and impede learning. Social interdependence theory suggests that social skills play an important role in enhancing collaboration and resolving conflicts. Data were collected through online questionnaires and follow-up interviews. Interview data were analyzed using a qualitative data analysis approach. The survey data were analyzed using multi-level structural equation modeling, which allowed us to reveal an interesting relationship between group-level social skills and collaboration. Results suggest that different individual difference factors triggered each type of conflict, and most of the groups experienced more than one type of conflict simultaneously. Task and process conflicts were often transformed into relationship conflict, when social skills were lacking. Interestingly, group-level social skills were more influential than individual members' social skills in reducing intragroup conflict and enhancing collaboration.