Soil underpins the entire agricultural ecosystem and plays a major role in both production and in the ecosystem services that regulate production. Agroecological transition involves transforming farming systems by replacing synthetic inputs with ecosystem services. To support these efforts, assessment methods are needed to perform an initial diagnosis and evaluate the changes produced by the transition. Generally speaking, soil quality and health cannot be measured directly. Instead, a range of indirect environmental assessment indicators must be used. This article reviews the indicators available for assessing the impact of agricultural management on soil fertility, quality and health. For these factors, the most commonly used indicators are based on field measurements. We also look at the predictive indicators used by agronomists striving to improve cropping systems and design innovative systems. Deeper investigation is warranted into several areas, such as the reference value and the predictive quality of indicators in relation to ecosystem services like pest regulation.