In engineering higher education, it is challenging to integrate knowledge, critical thinking skills, and dispositions to solve problems, particularly among first year students with little experience in teamwork. The literature on pedagogical interventions that promote critical thinking skills such as metacognition and critical thinking dispositions, which would help engineering students develop lifelong learning and effective reasoning for solving complex problems in collaborative professional settings, is limited. Since cooperative learning has been pointed out by the literature in other fields as being one of the most powerful approaches to promote critical thinking, this article aims to analyze the effects of the cooperative learning method “Group Investigation” on metacognition and critical thinking dispositions and to understand the correlations between those two dimensions. A quasi-experimental research design with One-Group Pretest-Posttest, using the Metacognitive Awareness Inventory and Critical Thinking Dispositions Scale was developed, among 34 engineering first year’s students attending the course of industrial management at a Portuguese university during one semester. The results of the intervention were significantly positive in both dimensions of metacognition: regulation of cognition and knowledge of cognition. Regarding the critical thinking dispositions, we found positive effects in “self-confidence”. This cooperative learning approach facilitated and triggered an interdependent relationship between metacognition and critical thinking dispositions, more specifically between “open-mindedness” and most of the metacognition variables, especially those from procedural knowledge.