Long-term measurements across the soil profile are essential for understanding how agricultural management affects soil organic carbon (SOC) storage, accumulation, and vertical distribution. We analyzed a 40-year record (1984–2023) from the Farming Systems Trial in Pennsylvania, USA, comparing conventional (CNV), legume-based organic (LEG), and manure-based organic (MNR) cropping systems. Seven sampling events were used to evaluate long-term surface SOC trajectories, three campaigns included the complete 0–100 cm soil profile, and full- and reduced-tillage treatments were compared from 2008 onward. Surface SOC increasingly diverged among cropping systems over time (system × year: χ² = 35.0, P < 0.001). By 2023, SOC concentrations in the 0–20 cm layer were 2.46% in MNR, 2.30% in LEG, and 1.92% in CNV. Equivalent-soil-mass-corrected SOC stocks were 70.3, 65.7, and 54.7 Mg C ha⁻¹, respectively, corresponding to gains of 15.6 Mg C ha⁻¹ in MNR and 11.0 Mg C ha⁻¹ in LEG relative to CNV. Across the full 1 m profile, MNR and LEG stored 119.0 and 108.9 Mg C ha⁻¹, respectively, compared with 92.9 Mg C ha⁻¹ under CNV. The effect of cropping system varied strongly with soil depth (system × depth: χ² = 77.9, P < 0.001). In both 2021 and 2023, 91–94% of the additional SOC stored under the organic systems occurred within the upper 30 cm. Permanganate-oxidizable carbon followed the same vertical pattern, indicating that both total SOC and management-responsive carbon increased primarily within the surface and transition layers. Cropping-system diversification and organic inputs had a substantially greater influence on SOC than tillage intensity, which had no significant overall or system-dependent effect. These findings show that diversified organic cropping systems can produce substantial and persistent SOC gains over four decades. Full-profile sampling combined with equivalent-soil-mass accounting also clarifies where those gains occur, providing a stronger basis for evaluating agricultural soil-carbon storage.