Indicator-based monitoring tools are frequently applied for sustainability assessments, also in agriculture. However, many indicators focus on a rather restricted number of sustainability aspects such as economy or ecology. Moreover the choice of the indicator is rarely explained. The aim of our study was to develop an indicator-based monitoring tool for integrated farm sustainability - i.e. taking into account economic and ecological and social aspects - based on a supported vision of sustainable agriculture and using a set of relevant indicators. Hereby, specific attention was paid to aspects of communication and user-friendliness. Four methodological steps were considered: (i) translating the major principles of a supported vision of sustainable Flemish agriculture into concrete and relevant themes; (ii) designing indicators to monitor progress towards sustainability for each of those themes; (iii) aggregating the indicators into an integrated farm sustainability monitoring tool and (iv) applying the monitoring tool on a practical farm, as a first attempt at end-use validation. Stakeholder participation and expert consulting played an important part in each of these methodological steps. As a case study, the methodology was applied to Flemish dairy farms. As a result, we developed MOTIFS, a user-friendly and strongly communicative indicator-based monitoring tool that allows the measurement of progress towards integrated sustainable dairy farming systems and fits within a well-founded methodological framework. MOTIFS is based on the equality of the economic, ecological and social sustainability dimensions, and this equality is inherently built into the system. Through the applied methodology, we founded the selected themes and indicators and we avoided using indicators that are not relevant to the problem at hand.