Winter cover crops are increasingly used to maintain water quality and agroecosystem productivity. Cover crop incorporation influences transient soil microbial dynamics and nutrient availability at an early growth stage of subsequent crops. Short-term ([35 <= d) effects of cover crop incorporation on soil C pools and N availability were evaluated using sandy loam soils from organically and conventionally managed fields. Field and incubation experiments were designed to investigate whether cover crop incorporation had differential effects on C pools and how they were related to N mineralization. Labile C pools (soil carbohydrates and soil microbial biomass C [SMBC]) and coarse organic debris (COD) increased two- to threefold, whereas total organic C increased by only 20% by Day 7 after incorporation. The COD decreased faster than other C pools and best predicted SMBC (P 30% of N in cover crop residues was mineralized in both soils by Day 35 after incorporation, suggesting that manipulations of soil microbial dynamics and N mineralization in the short term can be of particular significance in synchronizing N release with the need of subsequent crops.