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The few available studies on maize biomass in soil of field experiments have shown that belowground maize biomass resides more than twice as long as aboveground residues. Our principal objective was to investigate the effect of maize crop residue incorporation on the long-term dynamics of soil organic carbon (SOC) for a selection of croplands with sandy to sandy loam texture in Flanders, Belgium. After a period of more than 20 years, we resampled 31 and 29 parcels that had either silage maize (MS, only belowground biomass input) or grain maize (MG, both above- and belowground biomass input) dominated crop rotations. Changes in maize-derived SOC (Cmaize) of MS and MG systems between 1993 and 2018 were evaluated by detecting SOC content and its δ13C value. In addition, a 140-day incubation experiment (at 20.5 °C) was carried out to compare the stability of Cmaize and the related nitrogen (N) mineralization between the MG and MS fields. After two decades, δ13C raised 2.4 and 2.6‰, while Cmaize increased 1.6 and 2.2 g kg−1 in MS and MG systems, respectively. The estimated average humification coefficient over this period of maize-C was 0.11 for the MS system, about twice as that of the MG system (0.06). This reconfirms findings of stronger contribution of belowground biomass versus aboveground residues to stabilized SOC pools over the medium to long term. By the end of the incubation, on average 10.4% and 11.6% of Cmaize had been decomposed in the MS and MG soils, respectively. These Cmaize mineralization rates were statistically equal for the two systems, which indicates that mainly belowground biomass remained in the soils. Also, net N mineralization was indifferent to the crop rotations (MS: 58.8 mg N kg−1 and MG: 52.6 mg N kg−1). To reconcile the two main observations in this study, we hypothesize that the lower preservation of shoot-C could be manifested on a shorter term. Detailed research is needed to determine the time scale of increased stabilization of root-C versus shoot-C under field conditions.