Monitoring soil health status is imperative to pursue sustainable agriculture. Aggregate stability (AS) is fundamental to define several soil functions and, therefore, physical soil health. The objectives of thisworkwere to (i) evaluate the effect of contrasting cropping systems on AS, soil (SOC) and particulate (POC) organic carbon, and anaerobic nitrogen (AN) both in bulk soil and in macroaggregates (MA), and (ii) assess the relationship between AS and AN both in bulk soil and in MA to facilitate soil physical health monitoring. Aggregate stability, AN, SOC and POC were evaluated at three depths (0–5, 5–20, and 0–20 cm) in a Mollisol of the Southeastern Argentinean Pampas under a long-term experiment of cropping systems (crop-pasture rotations under conventional tillage [CT] and no-tillage [NT]). Bulk-soil SOC and POC contents and AN showed the effect of cropping systems, especially the effect of crop-pasture rotation and at 0–5 cm depth. However, NT did not lead to SOC sequestration except at 0–5 cm depth. In turn, pastures in the rotation and NT improved AS. Bulk-soil AN explained 75, 41, and 71% of AS at 0–5, 5–20, and 0–20 cm depths, respectively, and provides an indication of AS status. Instead, AN in MA did not explain bulk-soil AS changes as much as bulk-soil AN, except at 0–5 cm depth. Therefore, it is not worth determining AN in MA. However, routine bulk-soil AN determination at 0–20 cm depth by producers to diagnose nitrogen soil fertility would also provide an additional valuable indication of AS status.