The purpose of this study was to investigate the quality, evolution, and position of university students’ argumentation about organic agriculture over a 4-week argument–critique–argument e-learning experience embedded in a first year university biology course. The participants (N = 43) were classified into three groups based on their epistemological views. Data collected from individual arguments, group deliberations, and individual critiques were coded and analyzed to establish the quality and evolution of argumentation. Results indicated significant improvement in the quality of their justifications between the first and second arguments. Post-hoc comparison of epistemological groups indicated that the more constructivist-oriented students had a greater significant evolution of their justifications than the more empiricist-oriented students, but there was no significant main effect for epistemological orientation. Qualitative analysis of the intervening critiques indicated that some students incorporated or used other students’ arguments or counter-arguments to change their position or to enhance the justification of their original position on organic agriculture, while others appeared to be locked into a confirmation-bias stance and search for evidence that supported their original position and disregarded contradictory evidence.