Over half of the mangroves in Indonesia have been degraded or converted for aquaculture. We assessed the consequences of management decisions by studying the effects of different management regimes on mangrove ecosystem services in Java, Indonesia. A novel typology of management regimes distinguishes five main categories: natural, low intensity use, high intensity use, mangroves converted for aquaculture and abandoned aquaculture. Eleven specific management regimes were distinguished, based on legal status, management activities and aquaculture indicators. We assessed and verified matching ecological characteristics per regime. We identified key ecosystem properties underpinning service provision and ‘state’ and ‘performance’ indicators for seven ecosystem services: food, raw materials, coastal protection, carbon sequestration, water purification, nursery and nature-based recreation. Service provision was estimated and scored for each regime by relating their ecological characteristics with ecosystem service indicators. Natural mangroves scored highest for most services, except for food. High food production in aquaculture occurs at the expense of other services. Transitions between management regimes were illustrated to show consequences of management decisions. This study shows the merits of quantifying multifunctionality of management regimes in mangrove systems. Our findings contributed to a common vision among Javanese decision makers to include mangrove ecosystem services in their sustainable coastal management plan.