This study investigated whether a social-emotional learning program, implemented over a one-year period, could lead to gains in social-emotional competencies and to a reduction in internalizing and externalizing problems in the context of the COVID-19 pandemic. Furthermore, the program analyzed how students (boys vs. girls) with varying levels of social-emotional competencies and externalizing and internalizing problems, and from different socioeconomic backgrounds, were differently affected. The program was applied to 358 Portuguese third- and fourth-grade students (51.4% boys, Mage = 8.56; SD = 0.82). Self-report (students) and hetero-report (teachers) questionnaires were administered before and after the intervention. Linear mixed-effects models were computed to test intervention impacts. Significant intervention gains were noted in social-emotional learning competencies, namely emotional knowledge, social competence, peer relations, self-management, and academic behavior, and in externalizing (social problems) and internalizing (anxiety) problems. No effects were found in aggressiveness. Students with lower social-emotional competencies and higher externalizing and internalizing problems at baseline profited more from the program. Gender moderated both emotional knowledge and social problems, and socioeconomic status only moderated social problems. Findings highlight the effectiveness of this social-emotional learning program, especially for students facing initial challenges. Recommendations for future research, acknowledging limitations and strengths, are discussed.