Childhood obesity is an important public health issue influenced by both personal and environmental factors. The childcare setting plays an important role in children’s energy balance-related behaviours (EBRB), such as physical activity, sedentary behaviour and healthy nutrition. This study aimed to explore facilitators and barriers of healthy EBRB in childcare in a comprehensive way, from the perspective of three crucial stakeholders: childcare managers, childcare workers and parents. A qualitative study was performed using semi-structured interviews. Content analysis was performed using the ‘Environmental Research framework for weight Gain prevention’ (EnRG framework) to guide the analysis. Forty-eight interviews were held with a total of 65 participants (9 childcare managers, 23 childcare workers and 33 parents). Influential factors in all types of environment (physical, sociocultural, economic and political) were mentioned. Although a need for change was not always expressed, the interviews revealed opportunities for improvement of healthy EBRB in childcare. These opportunities were related to the sociocultural, physical and political environment. Childcare workers and managers expressed an influence of the home setting on the childcare setting, resulting in a need for more congruence between these settings. There are opportunities for improvement in the childcare setting to promote healthy EBRB in young children in the Netherlands. It appears important to align intervention components between the childcare and home setting.