Management practices can affect strongly the quality of agricultural soil. One tool that may assist in sustainable farm management is life cycle (impact) assessment (LC(I)A). However, under the area of protection (AoP) natural resources, effects of land use on soil quality are rather poorly addressed. Additional LCIA methods are therefore needed to evaluate the impact of agricultural land use practices (LUP) on soil quality. In this study, we introduce three interdependent indicators which are situated along the cause-effect chain accounting for the effect of LUP on soil quality in relation to the AoP natural resources. As soil organic carbon (SOC) is a key feature of soil health and fertility, we describe soil quality in terms of the change in SOC stock and the corresponding change in yield. At midpoint, the indicators SOC change (SOC2) and biomass productivity loss (BPL), are proposed to indicate losses in SOC and yield, respectively, due to farm management choices. At endpoint, the indicator additional land requirement (ALR) is introduced to indicate the need of extra agricultural area necessary for provisioning of the lost biomass yield. Characterization factors were developed for a case study in Flanders. Different soil textures, initial SOC stocks, crop rotation systems and LUP were considered. Because the reference state is based on sustainable LUP, the developed framework may serve as a decision support tool towards a more sustainable agriculture.