The increasing diversity in cities and schools is a pan-European experience. Concurrently, the time of subsequent crises (migration/refugee crises) has had severe impacts on the key institutions safeguarding the rights and needs of citizens. This also concerns the youngest generation in the education system, especially in the light of data concerning the still high and even growing rates of child poverty in Europe. Therefore, focusing on finding common solutions to early educational inequalities has become one of the key issues of research in the area of early childhood education. Diversity enables us to learn about conditions that may increase the effectiveness and desirability of early childhood education and care (ECEC) for children at risk, be it due to economic strain, possessing a migration background, disability and so forth. At the same time, however, it poses a methodological challenge due to the different construction of child welfare and education systems, the different policies and social solutions promoted and, last but not least, the different dimensions of the aforementioned diversity, namely ethnic, social or disability. This article discusses methodological challenges and strategies in an international and interdisciplinary project on combined inequalities among children in ECEC settings. The objective is to demonstrate how mixed-methods can be used for interdisciplinary interventions, connecting social research to the broader impact on the community.