Agricultural soil quality (SQ) research has focused on the influence of individual soil properties, particularly those related to soil organic matter (SOM), on soil processes such as water movement and retention, and nutrient cycling. However, few studies have assessed the influence of these SOM-related properties on crop productivity, particularly under different management systems. Furthermore, agricultural SQ research in tropical regions is limited. The objectives of this study were, for a tropical site, to determine (1) the relationship between selected soil characteristics and resulting soil functional properties such as aggregate stability and porosity, and (2) the relationship between SQ indicators and productivity of corn under three different tillage systems. Twelve plots were randomly demarcated in three adjacent fields under different tillage systems. Profiles were described by augering and the surface soil (0–7.5 cm) was sampled just prior to crop harvest and analyzed for texture, standard soil tests (pH, available P, K, Mg and Ca) and SQ parameters including total N, total and active fraction C, porosity and aggregate stability. Corn dry grain m−2, above-ground crop dry matter m−2, and dry grain per plant was measured in each plot. Soil C parameters were highly predictive of macroaggregate stability and soil porosity across different tillage systems. Macroaggregate stability and soil C (particularly active C oxidizable by 0.025m KMnO4) were highly correlated with crop productivity across tillage systems. These findings suggest that soil C in the surface layer, especially the active C fraction, markedly affected the productivity of this tropical soil through its influence on soil structure.