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In this longitudinal, observational study, following 883 adolescents (aged 11–15 years, grades 6th - 8th) we tracked changes in perceived school motivation and effort across four time points during the two years of remote education in Perú as a consequence of COVID-19 (retrospective reports before the pandemic, May 2020, July 2021, and November 2021). Compared to before the pandemic, levels of perceived school motivation and effort dropped sharply in May 2020 and continued to decrease across 2 years. Perceived school motivation was positively associated with perceived school effort at almost all time points. Furthermore, students with lower levels of perceived school motivation had a steeper decline in perceived school effort. In a subsample of 380 students in 8th grade, perceived school effort in July 2021 predicted objective math performance in November 2021. Our findings suggest that COVID-19 has further compounded decreases in subjective and objective indices of school engagement and performance that are typically observed in early adolescence. Our results from a large sample of low- to middle-class Peruvian adolescents highlight the experiences of youth in a country that had particularly long school closures, and that is under-represented in the literature. • Four time point longitudinal study of school motivation and effort with a large sample of low and middle income Peruvian adolescents during the COVID-19 pandemic • Perceived levels of school motivation and effort dropped sharply in May 2020, just after the pandemic started, and continued to decrease across 2 years of remote instruction • Lower subjective effort was associated with worse objective math performance [ABSTRACT FROM AUTHOR]