Improving population health and reducing inequalities through better integrated health and social care services is high up on the agenda of policymakers internationally. In recent years, regional cross-domain partnerships have emerged in several countries, which aim to achieve better population health, quality of care and a reduction in the per capita costs. These cross-domain partnerships aim to have a strong data foundation and are committed to continuous learning in which data plays an essential role. This paper describes our approach towards the development of the regional integrative population-based data infrastructure Extramural LUMC (Leiden University Medical Center) Academic Network (ELAN), in which we linked routinely collected medical, social and public health data at the patient level from the greater The Hague and Leiden area. Furthermore, we discuss the methodological issues of routine care data and the lessons learned about privacy, legislation and reciprocities. The initiative presented in this paper is relevant for international researchers and policy-makers because a unique data infrastructure has been set up that contains data across different domains, providing insights into societal issues and scientific questions that are important for data driven population health management approaches.