This paper discusses how to incorporate the changes within an agroecosystem into sustainability assessment. We measured the sustainability of 86 organic coffee producers located in 4 municipalities of Sierra Madre of Chiapas, Mexico. Based on the MESMIS framework, a set of indicators was selected. A sustainability index was constructed using the multi-criteria decision method known as the analytical hierarchy process in a broad participatory process with producers and cooperatives. Likewise, classification of producers was carried out through land use transitions in their lands between 1999 and 2019 using satellite imagery. A variance analysis between classes was performed to identify statistical differences. The results show that producers who expand their coffee plantations into forested areas have more sustainability levels than those producers who convert agricultural activities into coffee plantations and producers with both transitions in coffee expansion-conversion. The indicators of labor efficiency, benefit-to-cost ratio, price, remnant of primary vegetation, recovery of production from natural phenomena, family succession, and producer land area showed statistical differences between classes. These results are relevant because sustainability assessment is an action-oriented method. Therefore, the contribution of this study can help guide recommendations for specific groups of producers.