Abstract Purpose Since principles of conservation agriculture mimic the soil conditions of undisturbed natural soils, linking aggregation and dissolved organic matter (DOM) occlusion would therefore provide a targeted descriptor for soil health advances of innovative farming systems. This study aimed to assess structure-related DOM patterns of conservation farming systems and underlying bio-chemical drivers by using a novel method for the combined analysis of aggregate breakdown and DOM release. Methods Soil samples were collected from conventional farming, conservation farming and natural reference soil systems over a wide range of soil types. Ultrasonication aggregate breakdown combined with continuous UV–Vis measurement was used to characterize DOM release from soil. Measures of breakdown dynamics were related to soil physical and chemical properties to determine the strongest predictors of DOM release. Results The quantity of DOM released and aggregate stabilization showed a steady continuum starting from standard farming through conservation agriculture towards reference soil systems. DOM released from reference soils however was less complex and occluded in more stable soil aggregates than arable soils. The overall DOM release dynamics are shaped by agricultural management with site-specific modifiers driving aggregation and mineral-organic interactions in soils. Conclusions The simultaneous quantification of aggregate breakdown and DOM release captures key biophysical effects in structure-related DOM stabilization and revealed significant differences between land-use and agricultural management systems. The linkage of physical with functional soil organic matter descriptors provides an improved approach to monitor soil health advances in arable cropping systems.