The current study investigates the effects of the school lockdowns during school years 2019–2020 and 2020–2021 on the achievement scores of primary school students during the COVID-19 pandemic. We analyzed scores for spelling, reading fluency (i.e., decoding speed), reading comprehension, and mathematics from standardized student tracking systems for 5125 students from 26 primary schools in the urban region of The Hague, the Netherlands. Results showed that students in grades 1 through 3 had significant learning delays after the first lockdown. However, results after the second lockdown showed that most students were able to catch up, compared to students from corresponding grades of cohorts before COVID-19. The magnitude of these positive effects was mostly close to the negative effect of the first lockdown. Apparently, during the second lockdown, schools seemed better prepared and able to deliver more effective home schooling and online instruction. The hypothesis that students’ learning from a low SES home environment will suffer most from the school lockdowns could only partly be confirmed. SES effects at the individual level tended to be mitigated by negative effects of SES at the school level, making SES-related differences between schools less profound. The findings of this study offer a broader perspective to evaluate the effects of long-term school closures. Implications for educational practice and issues of inequality between students are discussed.