Recent studies have highlighted the critical role of manganese (Mn) in plant litter decomposition and soil organic carbon (C) cycling in forest ecosystems. Long term nitrogen (N) deposition and N fertilization can increase soil acidity and mobilize bioavailable Mn (Mn2+) in soil. However, no studies have examined the interactive effect of N and Mn fertilization on litter decomposition and carbon distribution in agricultural soils, despite agroecosystems being subject to both N and Mn management. We hypothesized that increased soil N and Mn availability would accelerate plant residue decomposition and transfer of its C to mineral-associated organic matter (MAOM), and that the combined effect of Mn and N enrichment would be greater than the individual effect. We conducted a laboratory incubation experiment by adding 13C-labeled residue of perennial grass Glyceria striata (Lam.) to agricultural soils that had received 225 kg N ha−1 yr−1 for 27 years (N1) and comparable soils that received no N (N0). Before the experiment, these soils also received three levels of dissolved Mn2+, designated M0 (no additional Mn), M1 (50 mg kg−1), or M2 (250 mg kg−1). We measured total CO2 production as well as distribution of 13C from the residue into CO2, particulate organic matter (POM), MAOM, and dissolved organic carbon (DOC) over a 1-year period. Manganese amendments significantly increased CO2 production from residue decomposition in the N1 soil, but no such effect was observed in the N0 soil. Manganese also accelerated the loss of residue-derived C from POM and DOC, but increased its recovery in MAOM. However, the positive effect of added Mn in decomposition and recovery in MAOM in the presence of N fertilization occurred only during the initial 30-day decomposition period, where M2 showed a 12% increase in cumulative CO2 production from residue, 8% increase in POM loss, and 43% increase in recovery of residue C in MAOM compared to M0. For M1, only CO2 emission from residue was significantly higher than Mo during this period. At 365 days M2 showed 8% increase in CO2 production, 1% increase in POM loss, and 16% increase in recovery of residue C in MAOM compared to M0, but none of these were statistically significant (p < 0.05). This study adds to the growing evidence that increasing Mn availability enhances plant litter decomposition. However, the occurrence and magnitude of Mn-induced stimulation of decomposition is context specific. Further investigation with greater temporal resolution, involving a multitude of litter and soil types and including microbial compositional and functional characterization, is recommended to fully elucidate the interactive role of Mn and N on C cycling.