Soil health is a term used to describe the general state or soil quality in an agroecosystem. The study of aggregate formation pathways has been successfully used to assess soil quality, especially chemistry, particularly in measuring the impact of different forms of use and management on soil health. This study aimed to (i) verify the contribution of biogenic (Bio) and physicogenic (Phy) aggregates to soil fertility; (ii) evaluate the total carbon (TC), nitrogen (TN), phosphorus (TP), and potassium contents and their respective stoichiometric ratios in these aggregates; and (iii) analyse the relationship between the P fractions (labile, moderately labile, and non-labile) and these aggregates. Three management systems were evaluated (permanent pasture, PP; no-tillage system, NT; and no-tillage + Urochloa system, NT+B) as well as a reference area (Atlantic Forest biome vegetation, NF). All the sample areas are located on soils with a sandy texture in the surface horizons. Aggregates were separated, identified, and classified according to their genesis into Bio (biotic factors) and Phy (abiotic factors). Only the PP system had significant increase in the values of TC, TN, TP, TK, and organic and inorganic P. The NT+B system favoured a proportional increase in TC content compared to the aggregates of the NF and NT areas, especially in the subsurface layer (ranging from 31 to 44%). For Bio aggregates, there were increments in TC and TN contents compared to Phy ones, especially in the NT and NT+B systems (8 to 30% for TC and 56 to 239% for TN). Bio aggregates also had the lowest values of C/N ratio in the surface layer (< 30), highest values of C/P ratio in the subsurface layer (> 33), and greater participation of the organic form of P in TP in the surface layer (between 26 and 42%). The chemical attributes in the aggregates were affected differently by the soil management systems, especially PP and NT+B systems. The results verified for Bio aggregates strengthen the hypothesis that these structural units are important sources of nutrients for the soil and reiterate the importance of studying the formation pathways in assessment soil health.