COVID-19 has had repercussions in economic, cultural, political, educational, family, and personal spheres due to the strategies implemented to stop its propagation. Against this background, the objective was to analyze the psychological alterations present during confinement and their impact on the academic performance of high school students in two institutions in Queretaro, Mexico. It was a descriptive, quantitative, and cross-sectional study in a sample of 428 students between 15 and 18 years of age (confidence level of 95 % and a 5 % error). The results show psychological alterations in cognitive processes (attention problems, disorganized thinking, and difficulty for virtual learning) and emotional processes (anxiety, stress, boredom, loss of enjoyment, sleeping problems, and need for peers), as well as the appearance of risky thoughts and behaviors (worthlessness, suicidal thought and attempts and self-harm). It is concluded that confinement caused significant cognitive and emotional alterations, which impacted academic performance (motivation, study habits), but not grades and homework submission.