A variety of established tools are available for agricultural sustainability assessment at global, regional, and farm geographical scales. However, no assessment has been reported in research literature to indicate their ability to provide insights about the most sustainable cropping system at plot level or experimental unit. Despite the environmental and social importance of soil in agricultural systems, many of the sustainability assessments use few or no indicators related to soil properties or processes. Hence, we propose a sustainability assessment methodology oriented to soil-associated agricultural experiments (SMAES) by defining its parameters through simulations and testing the methodology with real data from a fertilization tomato experiment with five treatments: chemical control (CR); organic control (OR); and organic:chemical ratios (OR) of 25:75, 50:50, and 75:25. The distance from the maximum, principal component analysis, and product of weighted indicator techniques were chosen for normalization, weighting, and aggregation in a single index process, respectively. Applying the SMAES methodology, the sustainability level of the treatments followed this sequence: CR (0.95) > O25:C75 (0.73) > O50:C50 (0.60) > O75:C25 (0.55) > OR (0.45). The proposed SMAES methodology allows soil researchers to define the best treatment through the interaction of the environmental, social, and economic dimensions of agricultural systems.