The COVID-19 pandemic has affected schooling worldwide. In many places, schools closed for weeks or months, only part of the student body could be educated at any one time, or students were taught online. Previous research discloses the relevance of schooling for the development of cognitive abilities. We therefore compared the intelligence test performance of 424 German secondary school students in Grades 7 to 9 (42% female) tested after the first six months of the COVID-19 pandemic (i.e., 2020 sample) to the results of two highly comparable student samples tested in 2002 (n = 1506) and 2012 (n = 197). The results revealed substantially and significantly lower intelligence test scores in the 2020 sample than in both the 2002 and 2012 samples. We retested the 2020 sample after another full school year of COVID-19-affected schooling in 2021. We found mean-level changes of typical magnitude, with no signs of catching up to previous cohorts or further declines in cognitive performance. Perceived stress during the pandemic did not affect changes in intelligence test results between the two measurements.