The aim of the present study was to analyze how family relationships changed during the COVID-19 pandemic and to determine whether the health crisis modified the association between family dimensions and emerging adult children’s mental health. A large sample of 1732 emerging adults was recruited at two different moments. In 2015, 755 emerging adults were recruited, 201 from campus A (sample 1) and 554 from campus B (sample 2). In 2020, a new sample was recruited and 977 emerging adults completed the questionnaire, 198 from campus A (sample 1 / “Pre-pandemic sample”, recruited before the lockdown) and 779 from campus B (sample 2 / “COVID-19 sample” / recruited after the lockdown. The results reveal that the COVID-19 sample of emerging adults perceived poorer parent-child relationships (lower parental involvement and warmth) and reported poorer mental health (lower flourishing and higher psychological distress) than their counterparts in Cohort 1. For their part, the Pre-pandemic sample reported higher levels of psychological distress than their counterparts in Cohort 1. In all samples (Cohort 1 and Cohort 2, both Pre-pandemic and COVID-19), parenting functions were positively associated with children’s flourishing and negatively associated with their psychological distress. However, these associations were stronger in Cohort 2 than in Cohort 1, both when assessed before and when assessed during the pandemic. The results of the study support the increasingly important role played by the family as a protective factor for mental health, even in stressful situations when family relationships tend to deteriorate. Study limitations include the use of a sample composed mainly of young emerging adult university students. Future studies should strive to include more emerging adults from the entire age range encompassed by emerging adulthood, as well as members of the non-university-going emerging adult population. Investing in public programs focused on family functions during emerging adulthood is an essential strategy for protecting and improving young adults’ mental health and promoting positive family relationships in stressful situations.