Abstract Purpose Tackling the global carbon deficit through soil organic carbon (SOC) sequestration in agricultural systems has been a focal point in recent years. However, we still lack a comprehensive understanding of actual on-farm SOC sequestration potentials in order to derive effective strategies. Methods Therefore, we chose 21 study sites in North-Eastern Austria covering a wide range of relevant arable soil types and determined SOC pool sizes (0–35 cm soil depth) in pioneer versus conventional management systems in relation to permanently covered reference soils. We evaluated physico-chemical predictors of SOC stocks and SOC quality differences between systems using Fourier-transform infrared (FTIR) spectroscopy. Results Compared to conventional farming systems, SOC stocks were 14.3 Mg ha^{− 1} or 15.7% higher in pioneer farming systems, equaling a SOC sequestration rate of 0.56 Mg ha^{− 1} yr^{− 1}. Reference soils however showed approximately 30 and 50% higher SOC stocks than pioneer and conventional farming systems, respectively. Nitrogen and dissolved organic carbon stocks showed similar patterns. While pioneer systems could close the SOC storage deficit in coarse-textured soils, SOC stocks in medium- and fine-textured soils were still 30–40% lower compared to the reference soils. SOC quality, as inferred by FTIR spectra, differed between land-use systems, yet to a lesser extent between cropping systems. Conclusions Innovative pioneer management alleviates SOC storage. Actual realized on-farm storage potentials are rather similar to estimated SOC sequestration potentials derived from field experiments and models. The SOC sequestration potential is governed by soil physico-chemical parameters. More on-farm approaches are necessary to evaluate close-to-reality SOC sequestration potentials in pioneer agroecosystems.