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Metacognition refers to how students monitor their cognitions and direct their learning. This study aimed to examine the relations between students’ self-perception of their performance and their brain activity during biological error reasoning. Thirty-four undergraduate students completed a model reasoning task during fMRI. Two distinct groups— Calibrated and non-Calibrated—were created based on their accuracy and reported confidence. General patterns indicated that participants tended to overestimate their performance. fMRI results demonstrated that Calibrated participants showed a higher change in brain activity in the right superior frontal gyrus than non-Calibrated, over-confident participants when reasoning about models that required them to identify errors. These findings highlight meta-cognition, and specifically students’ self-calibration, as a core target for STEM educators to promote effective reasoning.