Although the association of minerals and organic matter (OM) in soil plays an important role in the sequestration of C, the factors driving the initial formation of mineral-associated OM (MAOM), and thus the retention of new C input in soils are not yet fully understood. In this study, we investigated how the soil C loading and the differences in the N content of low-molecular-weight organic compound (LMWOC) input foster the rapid C retention in the soil's fine mineral fractions (clay and fine silt-sized fraction). Two topsoils (0–10 cm) with different C loading due to different long-term management (direct seeding vs. bare fallow) derived from an agricultural research trial were used for the short-term incubation experiment. In a 24-hour incubation experiment, we used two labeled substrates (without N, glucose, > 99% ¹³C and with N, amino acid mixture, > 98% ¹³C, > 98% ¹⁵N) to investigate how the different N content delivered by the LMWOC input determine the fate of newly formed OM in the MAOM pool. Our results show that the soil with low C loading and thus a low C saturation level retained more freshly added LMWOC in the fine MAOM pool compared to the high C-loading soil, demonstrating that the soil C loading is a major factor controlling the retention of freshly added OM at the early stage of MAOM formation. The LMW OM containing N significantly enhanced the recovery of freshly added LMWOC in the low C-loading soil but not in the high C-loading soil. This points to the great importance of the N availability for the retention of freshly added OM in soils. Our study showed that the level of the native OM content affects the fast retention of freshly added OM in the clay-sized fraction to a greater extent than the N availability of the OM substrate.