Metacognition is a key concept in the field of education. Some studies showed that metacognitive programmes can benefit students’ academic success, particularly for struggling students who lack awareness of their weaknesses or efficient strategies. In this vein, our study aims to take into account the cognitive profile of middle-school French students who received the metacognitive educational programme Cogni’Scol. Using cluster analysis, we investigated the cognitive profiles of 87 middle-school students based on the alignment between their self-efficacy, cognitive measures, and their actual academic performance, whether they received the programme or not over 2 years. According to the cognitive profile and group (experimental vs. control), we then analysed the differential effects of the Cogni’Scol programme on students’ success in reading and mathematics tasks as well as on their calibration of self-efficacy with academic performance. Firstly, we identified four student cognitive profiles by integrating factors known to influence academic success (self-efficacy, memory, intellectual, executive, and metacognitive abilities), which have never been considered together in previous profiling studies. Secondly, the Cogni’Scol programme seems to promote only the calibration of self-efficacy with academic performance of some struggling students. We discuss some theoretical and methodological implications for future research.