Inquiry includes a broad spectrum of approaches, depending on students' responsibility over the process and the extent of the teacher's guidance. While numerous studies have examined students' achievements and engagement across different types of inquiry-based environments, analyses of teachers' guidance during the process are lacking. Therefore, our overarching goal was to examine the interplay between characteristics of the inquiry-based environment and teacher's just-in-time support. Specifically, we examined the learning processes and achievements of middle-school students as they collaboratively engaged in either a "structured" or a "guided" inquiry-based task and were supported by their teacher. "Structuring" scaffolds were designed to support the structured inquiry task, while "problematizing" scaffolds were designed to support the guided inquiry task. Post-test scores indicated a similar significant increase in students' scientific understanding for both research conditions, despite significant differences in students' engagement in metacognitive processes during their scientific trials. Students from the guided inquiry group engaged in longer discussions and made more references to metacognitive processes, in comparison to students from the structured inquiry group. A low to moderate correlation between students' engagement in metacognitive processes and test-scores was identified. The teacher's regulation of students' discourse in the structured inquiry group was significantly greater than in the guided inquiry group, though the nature of regulation was similar. We propose that the teacher's regulation of students' metacognitive discourse outweighed the differences between students' learning processes in the two learning environments, resulting in similar achievements in the two conditions albeit differences in metacognitive engagement. Implications are discussed.