Engaging students in inquiry is a key component in order to fulfill essential goals in science education. To achieve successful engagement in inquiry process, students need to feel competent and autonomous in spite of the cognitive and mental challenges the process entails. The study focuses on the "problematizing" mechanisms of scaffolds and highlights the centrality of metacognition in the inquiry process. The study's primary goal was to examine how providing students involved in inquiry with individual, social, or a combination of both metacognitive scaffoldings affected their expressions of competence and autonomy. Using both qualitative and quantitative methods, we examined middle-school students' expressions of competence and autonomy in an online asynchronous forum that accompanied a year-long socio-scientific inquiry process. The process included four research conditions which differed by the metacognitive scaffolding students received: only individual, only social, both individual and social, and no metacognitive scaffolds. Although no significance difference was observed in students' expressions of competence in the initial phases of the inquiry among the research groups, students who received individual or social metacognitive scaffolding increased these expressions as they progressed through the process. Expressions of competence by students who received a combination of both types of support remained constant. In contrast, a significant decrease in students' expressions of competence was observed in the control group. Regarding autonomy, students' expressions of autonomy from all scaffolded conditions remained constant throughout the inquiry process, except for a significant decrease, experienced by students in the control group. The results are discussed through the lens of problematizing mechanism by which metacognitive scaffolding operate.