Collaborative argumentation has been recognized as a powerful means to facilitate conceptual change of scientific concepts for which students have robust misconceptions. However, eliciting and maintaining collaborative argumentation that yields such productive outcomes is known to be difficult. Specifically, social-motivational antecedents have not yet been explored. Over 13 weeks, we conducted a controlled experiment to examine the role of achievement goals in productive collaborative argumentation in the context of scientific concept learning while fully considering the effects on conceptual change, argumentative discourse, and perceptions of conflicts. Three types of achievement goals were identified among 94 undergraduates: mastery goal-dominant (a focus on developing competence and task mastery), two goals-balanced (pursuing mastery and performance goals simultaneously) and performance goal-dominant (a focus on demonstrating competence relative to others). Eighteen homogeneous groups participated in four collaborative argumentation activities concerning four scientific topics of varying controversy levels. The results showed that for highly controversial topics, mastery goal-dominant students and two goals-balanced students exhibited greater conceptual change than performance goal-dominant students over a longer period. Dialogue protocol analysis further revealed a combined pattern of argumentative discourse (i.e., both deliberative argumentation and co-consensual construction frequently occurred, while disputative argumentation rarely occurred) among mastery goal-dominant students and two goals-balanced students concerning highly controversial topics. Responses to stimulated recall interviews also indicated that perceptions of conflicts among the three types of students differed in terms of five aspects: their first impression of disagreements, their feelings in response to peer disagreement, their reasons for changing or maintaining to their original ideas, the meaning of group consensus, and the degrees to which they accepted group consensus. This study sheds light on the role of social-motivational antecedents, deepening our understanding of whether different achievement goals might orient students to different perceptions of conflicts, triggering different argumentative discourse, producing different conceptual change.