Frameworks describing the overall assessment of sustainability are limited and usually not well described. This study proposes a protocol for the selection and quantification of indicators that can be used to discuss and communicate the sustainability of agri-food production systems. A gross list of indicators was established covering the social, environmental and economic dimensions. Core indicators were selected from this gross list using predefined criteria. Then, sustainability limits were set for these core indicators to evaluate their sustainability impact. Policy makers can determine the effects of different weights and the extent to which indicators can compensate each other (compensability) either at the level of the individual indicator or on the overall sustainability. The protocol was tested in a case study comparing potato production in peri-urban agriculture to conventional and to organic agriculture. Data were based on literature, expert opinion and additional calculations. Application in the case study showed that the protocol can be a valuable tool in assessing the sustainability of agri-food production systems. It enables more transparent policy decisions and facilitates communication with stakeholders about these decisions.