This study attempts to investigate through causal-comparative research whether socio-scientific argumentation processes of prospective science teachers (PSTs) who had high and low socio-scientific argumentation skills differed from each other in terms of metacognition. The research was conducted with a total of 45 PSTs, 24of whom had high socio-scientific argumentation skills, and 21 had low socio-scientific argumentation skills. Data were gathered using qualitative and quantitative methods. Research results indicated that the PSTs with high socio-scientific argumentation skills displayed more metacognitive behaviors when compared to the PSTs with low socio-scientific argumentation skills and that they used more metacognitive strategies with regard to many components such as planning, decision-making, evaluation, monitoring, and organizing. Furthermore, a statistically significant difference was detected between the scores of the PSTs' metacognitive awareness skills in favor of the PSTs with high socio-scientific argumentation skills. These results demonstrated that the two groups with different socio-scientific argumentation skills differed from each other in terms of metacognition and that the PSTs with high socio-scientific argumentation skills were better in regard with metacognition.