Characteristics of early childhood education and care (ECEC) centers might be relevant for children’s health. This scoping review aims to provide an overview of the association between meso-level characteristics (MLCs) of ECEC centers with children’s health, health behavior, and wellbeing. Five databases were searched for quantitative and qualitative research articles published in English or German since 1 January 2000 on health, health behavior, and wellbeing of children aged 0 to 6 years considering MLCs of ECEC centers. Two authors screened 10,396 potentially eligible manuscripts and identified 117 papers, including 3077 examinations of the association between MLCs and children’s health indicators (Kappas > 0.91). Five categories of MLCs were identified: (1) structural characteristics, (2) equipment/furnishings, (3) location, (4) facilities/environment, (5) culture/activities/policies/practices, and 6) staff. Only very few studies found an association of MLCs with body weight/obesity, and general health and wellbeing. Especially physical activity and mental health were related to MLCs. In general, the location (rural vs. urban, neighborhood status) seemed to be a relevant health aspect. MLCs of ECEC centers appeared relevant for child health indicators to different degrees. Future research should focus on these associations, in detail, to identify concrete ECEC indicators that can support health promotion in early childhood.