Sustainable soil management practices are required in agriculture to enhance carbon sequestration and restore soil functions. Here, the aim was to investigate the effect of different tillage practices combined with or without irrigation on (i) soil organic carbon (SOC) content, (ii) fungal biomass and their relationships with aggregate size classes in the soil surface layer; further, (iii) the concept of soil particle saturation with SOC was tested to evaluate if a threshold was reached in a 14 year-experiment. Our hypothesis was that long-term irrigation, intensive tillage and their combination, would negatively affect soil aggregation and SOC stabilization. The experiment has started in 2003 on a research farm in Canterbury, New Zealand. The present work focused on two contrasting tillage practices –intensive tillage with 20–25 cm ploughing (IT) and direct drill (DD)– combined with sprinkler-irrigated and non-irrigated (hereafter called Rainfed) conditions in a split-plot experimental design. Soil samples (0–5 cm layer) were analyzed for pore size distribution, specific surface area and microbial biomass. Further, wet sieving was used to isolate large macroaggregates (LM, > 2000 μm), small macroaggregates (SM, 250–2000 μm), microaggregates (m, 53–250 μm), particle sized silt + clay fractions (s+c, < 53 μm) and Fine20 particles (<20 μm), followed by the analysis of aggregate morphology and SOC quantification in them. Results showed that both DD and Rainfed management increased total SOC content of the bulk soil. Only the LM fraction and the SOC therein (OC-LM) increased significantly in DD compared to IT, while m and s+c fractions and OC-m and OC-s+c did not differ between treatments. Macroaggregate breakdown processes and measured SOC therein had likely not reached steady-state conditions, as suggested by the lack of any SOC differences in the aggregate size classes < 250 µm. In contrast, the Fines20:SOC ratio differentiated between soils that had reached (i.e., DD) or not reached (i.e., IT) the saturation threshold. Finally, it was observed that a higher fungal:bacteria (F:B) ratio was generally accompanied by a greater LM fraction and mean weight aggregate diameter, highlighting the importance of fungi in the formation of LM. These results suggested that our hypothesis of detrimental effects on soil aggregation and SOC accumulation of both tillage and irrigation was not fully demonstrated yet. A longer study period would be required to better understand the effects of such practices of SOC storage.