Quantifying long-term soil organic carbon (SOC) dynamics in croplands is critical to evaluate their climate mitigation potential. We assessed SOC stock changes over 21 years at the BE-Lon ICOS cropland (Belgium) by comparing decadal soil inventories, RothC model simulations, and eddy covariance (EC) flux measurements, supported by comprehensive uncertainty propagation. Soil inventories and RothC indicated near-equilibrium SOC stock dynamics, with a non-significant loss and a gain of 19.7 ± 30.3 gC m⁻² yr⁻¹, respectively. In contrast, EC-derived carbon budgets suggested mean annual SOC losses of 69.8 ± 19.2 gC m⁻² yr⁻¹. Uncertainty in the flux-based approach was distributed evenly among spectral corrections, friction velocity thresholds, and lateral carbon flux estimates; yet it remained substantially smaller than the cumulative flux signal. A systematic positive discrepancy between EC-derived budget and RothC simulations suggests an underestimation of net carbon sequestration by the EC technique, which is consistent with the well-documented energy balance non-closure at cropland sites. Despite these methodological discrepancies, both EC and RothC consistently highlighted the critical role of management practices. Notably, both approaches identified the winter wheat–cover crop sequence as a moderate net carbon source in the absence of organic amendments. Conversely, manure application emerged as the primary driver of SOC stock accumulation. More broadly, this study highlights the necessity of combining process-based models, multi-decadal inventories, and EC flux measurements to reliably constrain SOC budgets and identify robust management drivers in cropland ecosystems.