Type and rate of fertilizers influence the level of soil organic carbon (Corg) and total nitrogen (Nt) markedly, but the effect on partitioning of C and N into different pools is open to question. Objectives were to investigate the impact of fertilizer type and rate on labile, intermediate and passive C and N pools in a sandy Cambisol at Darmstadt, Germany, after 27 years of different fertilization treatments. The six treatments were: straw incorporation plus application of mineral fertilizer (MSI) and application of farmyard manure (FYM) each at high (140–150 kg N ha−1 year−1), medium (100 kg N ha−1 year−1) and low (50–60 kg N ha−1 year−1) rates. Soil microbial biomass C (Cmic) and N (Nmic) and C and net N mineralization (266 days incubation at 10°C and 50% waterfilled pore space) were determined. Soils (0–25 cm) of MSI treatments had significantly (p≤0.05) lower Cmic stocks (308–361 kg ha−1) than soils of FYM treatments (404–520 kg ha−1). Differences in Nmic stocks were less pronounced. After 266 days, mineralized C (1130–1820 kg ha−1) and N (90–125 kg ha−1) had significantly increased with fertilizer rate. The application of an exponential two-pool model showed that very labile pools (turnover times: 17 and 9 days for C and N, respectively) were small (1.3–1.8% of Corg and 0.5–1.0% of Nt) and not influenced by type or rate of fertilizer. Stocks of the modeled labile C and N pools (turnover times: 462 and 153 days for C and N, respectively) were not influenced by the type of fertilizer but depended significantly on the application rate and ranged from 7 to 13% of Corg and from 4 to 5% of Nt. In contrast, the size of the calculated intermediate C pool was greater for the FYM treatments, and depended significantly on the interaction of fertilizer type and rate. The intermediate N pool was unaffected by fertilizer type or rate. Passive C and N pools, as experimentally revealed by oxidation with disodium peroxodisulfate (Na2S2O8), were independent of the treatments. Overall, labile and intermediate pools were affected differently by the fertilizer type and the application rate.