Differences in the mechanisms of storage and decomposition of organic matter (OM) between minimum tillage (MT) and conventional tillage (CT) are generally attributed to differences in the physical impact through tillage, but less is known about the effects of residue location. We conducted an incubation experiment at a water content of 60% of the maximum water-holding capacity and 15°C with soils from CT (0–25 cm tillage depth) and MT fields (0–5 cm tillage depth) with 15N-labeled maize straw incorporated to different depths (CT simulations: 0–15 cm; MT simulations: 0–5 cm) for 28 d in order to determine the effects of the tillage simulation on (1) mineralization of recently added residues, (2) the dynamics of macroaggregate formation and physical protection of OM, and (3) the partitioning of maize-derived C and N within soil OM fractions. The MT simulations showed lower relative C losses, and the amount of maize-C mineralized after 28 d of incubation was slightly but significantly lower in the MT simulations with maize added (MTmaize) than in the respective CT (CTmaize) simulations. The formation of new water-stable macroaggregates occurred during the phase of the highest microbial activity, with a maximum peak 8 d after the start of incubation. The newly formed macroaggregates were an important location for the short-term stabilization of C and N with a higher importance for MTmaize than for CTmaize simulations. In conclusion, our results suggest that a higher amount of OM in MT surface soils compared with CT surface soils may not only result from decreased macroaggregate destruction under reduced tillage but also from a higher efficiency of C retention due to a more concentrated residue input.