The new generation spend a considerable amount of their time in formal education settings. Only a small fraction of this time is allocated to equipping children with the ability to deal with sustainability issues and so empowering them to respond to the key challenges of our time. Systems thinking (ST) has been promoted as a way of responding to these challenges by facilitating the understanding of complex dilemmas and mitigating them. The aim of this multiple case study is to shed light on the impact of early childhood education (ECE) settings on the ST skills of preschool children aged between four and six. For this purpose, we developed a strategy and instruments to determine ECE setting variables that could potentially be taken into consideration in ST education. We applied this methodology to contrasting cases from Turkey and Germany. The findings have important implications for policy makers, researchers and ECE teachers.