After the lockdown, schools adopted measures to avoid infection, which changed pre-pandemic routines. We evaluated whether the new school conditions constituted a stress factor for children or contributed to their recovery after the impact of the lockdown period. Participants included 291 families with children between 3 and 11 years of age. The children were assessed by parents through the Child and Adolescent Assessment System (SENA) at three time points: T1 (before COVID-19 confinement), T2 (after the children had spent between 4 and 6 weeks confined), and T3 (one year after the beginning of the pandemic). For Preschoolers, no statistical differences were found in any scale or time point. For primary-school children, the differences between T1 and T3 were not significant. Comparisons between T2 and T3 showed significant differences in Willingness to study, Emotional regulation and Hyperactivity and impulsivity. Our results suggest that returning to school might have improved some dimensions of primary-school children’s well-being. However, it seems that neither the confinement nor the restrictive measures have had a negative effect on our sample. To interpret these findings, we discuss the psychological factors of protection and vulnerability.