More and more often, we hear that higher education should foment critical thinking. The new skills focus for university teaching grants a central role to critical thinking in new study plans; however, using these skills well requires a certain degree of conscientiousness and its regulation. Metacognition therefore plays a crucial role in developing critical thinking and consists of a person being aware of their own thinking processes in order to improve them for better knowledge acquisition. Critical thinking depends on these metacognitive mechanisms functioning well, being conscious of the processes, actions, and emotions in play, and thereby having the chance to understand what has not been done well and correcting it. Even when there is evidence of the relation between metacognitive processes and critical thinking, there are still few initiatives which seek to clarify which process determines which other one, or whether there is interdependence between both. What we present in this study is therefore an intervention proposal to develop critical thinking and meta knowledge skills. In this context, Problem-Based Learning is a useful tool to develop these skills in higher education. The ARDESOS-DIAPROVE program seeks to foment critical thinking via metacognition and Problem-Based Learning methodology. It is known that learning quality improves when students apply metacognition; it is also known that effective problem-solving depends not only on critical thinking, but also on the skill of realization, and of cognitive and non-cognitive regulation. The study presented hereinafter therefore has the fundamental objective of showing whether instruction in critical thinking (ARDESOS-DIAPROVE) influences students’ metacognitive processes. One consequence of this is that critical thinking improves with the use of metacognition. The sample was comprised of first-year psychology students at Public University of the North of Spain who were undergoing the aforementioned program; PENCRISAL was used to evaluate critical thinking skills and the Metacognitive Activities Inventory (MAI) for evaluating metacognition. We expected an increase in critical thinking scores and metacognition following this intervention. As a conclusion, we indicate actions to incentivize metacognitive work among participants, both individually via reflective questions and decision diagrams, and at the interactional level with dialogues and reflective debates which strengthen critical thinking.