Disturbed grassland soils are often cited as having the potential to store large amounts of carbon (C). Fertilization of grasslands can promote soil C storage, but little is known about the generation of recalcitrant pools of soil organic matter (SOM) with management treatments, which is critical for long-term soil C storage. We used a combination of soil incubations, size fractionation and acid hydrolysis of SOM, [C], [N], and stable isotopic analyses, and biomass quality indices to examine how fertilization and haying can impact SOM dynamics in Kansan grassland soils. Fertilized soils possessed 113% of the C possessed by soils subjected to other treatments, an increase predominantly harbored in the largest size fraction (212-2,000 μm). This fraction is frequently associated with more labile material. Haying and fertilization/haying, treatments that more accurately mimic true management techniques, did not induce any increase in soil C. The difference in 15N-enrichment between size fractions was consistent with a decoupling of SOM processing between pools with fertilization, congruent with gains of SOM in the largest size fraction promoted by fertilization not moving readily into smaller fractions that frequently harbor more recalcitrant material. Litterfall and root biomass C inputs increased 104% with fertilization over control plots, and this material possessed lower C:N ratios. Models of incubation mineralization kinetics indicate that fertilized soils have larger pools of labile organic C. Model estimates of turnover rates of the labile and recalcitrant C pools did not differ between treatments (65.5 ± 7.2 and 2.9 ± 0.3 μg C d−1, respectively). Although fertilization may promote greater organic inputs into these soils, much of that material is transformed into relatively labile forms of soil C; these data highlight the challenges of managing grasslands for long-term soil C sequestration.