In Portugal, early childhood education and care services for children under-three were the first educational services to reopen after periods of lockdown. COVID-19 prevention and control measures had to be implemented nationwide, but no knowledge was yet produced on their impact in educational settings. This study aimed to map the implementation of COVID-19 prevention and control measures and examine associations among prevention and control measures, perceived changes to pedagogical practices and children's well-being in early childhood education and care services for children under three. In this study, 1098 early childhood education and care professionals from all districts completed an online survey during January and February 2021. Results indicated that prevention and control measures were widely implemented. Furthermore, early childhood education and care professionals who started to implement prevention and control measures more frequently were more likely to perceive a reinforcement of their pedagogical practices at the level of adult-child interaction, emotional climate, and interaction with families, and reported higher levels of children's well-being. Findings highlighted the potential role of pedagogical practices in mitigating the effects of COVID-19 in early childhood education and care services for children under-three.