Background: Recent research has illustrated the need for cross-sector partnerships to tackle multidimensional problems such as health inequalities and sport and physical activity promotion. Capacity building is based on partnerships and has demonstrated effectiveness in tackling these multidimensional problems. This study aims to explain how cross-sector partnerships build capacity at the practitioner, organisational and partnership levels. The subject of this study is a community sport program (CSP) that aims to increase sport participation rates and physical activity levels. Methods: The study examined multiple cases in four disadvantaged communities in Antwerp, Belgium where the CSP was implemented. Forty-four face-to-face interviews were held with leaders from sport, social, health, culture and youth organisations that collaborated with the CSP. Results: Thirteen elements of cross-sector partnerships were identified as critical to building capacity at each of the different levels. These include: process evaluation, trust, mutuality, policy support, partner complementarity and fit, diversity of activities and period of collaboration-time. Trust in turn was fostered by a longer period of collaboration-time, better personal contact, clearer coordination and an external focus. Policy support was developed by support of partners and establishing clear metrics of success. Conclusion: Insight into the key elements of cross-sector partnerships that build capacity is given and several practical recommendations are suggested for practitioners and policy makers.