Analyses of short-term decomposition of labelled mustard litter in different field areas of an agricultural cropland lead to a better understanding of small-scale differences in organic matter turnover. High Yield (HY) areas of an agricultural cropland were characterized by different positions on a slope and lower silt and clay contents, compared to Low Yield (LY) areas, and this was associated with differences in water regime and OC and N turnover. To understand differences in OC and N flows of HY and LY areas, a combination of ¹³C / ¹⁵N tracer techniques and physical fractionation procedures was applied. Labelled plots as well as control plots were set up in both HY and LY field areas. Soil samples of the A horizon were taken in intervals of 4 to 6 months within the following two years. The samples were physically fractionated with a combined size and density fractionation procedure, resulting in mineral associated sand-, silt-, and clay-sized organic matter fractions, and in not-mineral associated Particulate Organic Matter fractions (POM). The small-scale differences in the local soil characteristics result in faster and more intensive POM decomposition in HY soils within the first year after mustard litter application. In LY soils, higher amounts of POM-OC and POM-N occluded in macroaggregates were found, attributable to a more intensive aggregate turnover and leading to a closer contact between POM and mineral surfaces in this area. However, after two years, the remaining ¹⁵N and ¹³C amounts in POM fractions of both areas are similar, due to faster decomposition of labelled POM in LY soils in the second year. 570 days after start of the experiment, only 2.5% of the initial ¹⁵N amount, but up to 10% of the initial ¹³C amount was found in POM fractions, with higher amounts in POM occluded in aggregates than in free POM. After this period, stabilisation of the initial ¹⁵N in fine silt- and clay-sized fractions amounts to 10% in HY, but 20% in LY soils. Compared to ¹⁵N, added ¹³C shows a lower recovery in the fine mineral fractions, with 8% in HY and LY soils after 570 and 160 days, respectively. The higher silt and clay contents of LY areas seem to promote N stabilisation in fine mineral fractions, but do not promote the stabilisation of OC. Summarized, N shows preferred release from the POM fraction and is partly stabilized in the fine mineral fractions, whereas OC is more persistent in the POM fractions. In terms of N availability, we can conclude for HY areas that a higher release of N in combination with lower storage of the added N in fine mineral fractions leads to better N availability for plant growth, but may also enhance the microbial biomass. This, in turn, may increase OM degradation, leading to the risk of higher N losses due to leaching or denitrification processes.