This study investigated the repercussions of coronavirus disease (COVID-19) and the subsequent quarantine on the emotional well-being of children in their initial years of formal schooling, with particular emphasis on children with special educational needs (SEN) and children from high and low socioeconomic statuses (SES). This longitudinal study employed the Child Behavior Checklist for ages 6-18 (CBCL) completed by the students' guardians at least once during 2018-2019 and again during 2020. The results showed differences in internalizing and externalizing problems after 8 months of quarantine and a significant increase in students fitting clinical or borderline categories given by the CBCL itself. The results are described in detail for four groups considering the combination of SEN and SES characteristics, showing the importance of their intersectionality, especially between low SES and SEN.