Characteristics of the physical childcare environment are associated with children’s sedentary behavior (SB) and physical activity (PA) levels. This study examines whether these associations are moderated by child characteristics. A total of 152 1- to 3-year-old children from 22 Dutch childcare centers participated in the study. Trained research assistants observed the physical childcare environment, using the Environment and Policy Assessment Observation (EPAO) protocol. Child characteristics (age, gender, temperament and weight status) were assessed using parental questionnaires. Child SB and PA was assessed using Actigraph GT3X+ accelerometers. Linear regression analyses including interaction terms were used to examine moderation of associations between the childcare environment and child SB and PA. Natural elements and portable outdoor equipment were associated with less SB and more PA. In addition, older children, boys and heavier children were less sedentary and more active, while more use of childcare and an anxious temperament were associated with more SB. There were various interactions between environmental factors and child characteristics. Specific physical elements (e.g., natural elements) were especially beneficial for vulnerable children (i.e., anxious, overactive, depressive/withdrawn, overweight). The current study shows the importance of the physical childcare environment in lowering SB and promoting PA in very young children in general, and vulnerable children specifically. Moderation by child characteristics shows the urgency of shaping childcare centers that promote PA in all children, increasing equity in PA promotion in childcare.