This paper presents the findings of longitudinal research conducted in Ethiopia exploring the effects of COVID-19 school closures on children’s holistic learning, including their socioemotional and academic learning. It draws on data from over 2,000 pupils captured in 2019 and 2021 to compare primary school children’s dropout and learning before and after school closures. The study adapts self-reporting scales used in similar contexts to measure grade 4–6 pupils’ social skills and numeracy. Findings highlight the risk of widening inequality regarding educational access and outcomes, related to pupils’ gender, age, wealth and location. They also highlight a decline in social skills following school closures and identify a positive and significant relationship between pupils’ social skills and numeracy over time. In conclusion, we recommend a need for education systems to promote children’s holistic learning, which is even more vital in the aftermath of the pandemic.