This cross-sectional study (conducted in April–May 2011) explored associations between partnership functioning synergy and sustainability of innovative programmes in community care. The study sample consisted of 106 professionals (of 244 individuals contacted) participating in 21 partnerships that implemented different innovative community care programmes in Rotterdam, The Netherlands. Partnership functioning was evaluated by assessing leadership, resources administration and efficiency. Synergy was considered the proximal outcome of partnership functioning, which, in turn, influenced the achievement of programme sustainability. On a 5-point scale of increasing sustainability, mean sustainability scores ranged from 1.9 to 4.9. The results of the regression analysis demonstrated that sustainability was positively influenced by leadership (standardised regression coefficient β = 0.32; P < 0.001) and non-financial resources (β = 0.25; P = 0.008). No significant relationship was found between administration or efficiency and programme sustainability. Partnership synergy acted as a mediator for partnership functioning and significantly affected sustainability (β = 0.39; P < 0.001). These findings suggest that the sustainability of innovative programmes in community care is achieved more readily when synergy is created between partners. Synergy was more likely to emerge with boundary-spanning leaders, who understood and appreciated partners’ different perspectives, and could bridge their diverse cultures and were comfortable sharing ideas, resources and power. In addition, the acknowledgement of and ability to use members’ resources were found to be valuable in engaging partners’ involvement and achieving synergy in community care partnerships.