Abstract The bioenergy economy promises to stimulate the local economic growth and improve the welfare of people living in rural areas. To accomplish this, there is global consensus on the sustainability indicators that must be evaluated in bioenergy production systems (BPSs). However, the utilization of these indicators has several constraints, such as their interpretation and application in developing countries in addition to the inherent complexity of BPSs. Here, we propose a sustainability framework applicable to BPSs. First, we use the framework for assessing the sustainability of the natural resource management systems (MESMIS) methodology to define a BPS and derive economic, environmental and social indicators. After that, we use the distance-to-target weighting method to describe a sustainability gradient of five levels for each indicator. Finally, we use the sustainability gradient to normalize the indicators and thereby weight and aggregate the indicators into a sustainability index (SI). After the application of the MESMIS methodology, a BPS was defined as three interrelated subsystems; 1) the biomass subsystem dedicated to the feedstock supply; 2) the transformation subsystem dedicated to convert the feedstock into bioenergy; and 3) the social subsystem that provides the workforce. This sustainability framework allows comparing two (or more) BPSs in cross-sectional and longitudinal studies. A total of 7 economic indicators, 10 environmental indicators and 11 social indicators were described in terms of a sustainability gradient. The sustainability gradient converts the indicators to comparable units. Then, we propose to aggregate these indicators into three subindices by evaluated area: an economic subindex, an environmental subindex, and a social subindex. Each subindex ranges from 0 for an unsustainable BPS to 5 for a highly sustainable BPS. The SI integrates these three subindices, giving the same relevance to the economic, environmental and social areas.