Adding high quantities of organic matter can increase carbon (C) inputs to soil and help maintain soil structure. This study investigated short-term effects of application of different levels of composted dairy manure (CDM) versus interseeding a legume into grass pasture on aggregate stability and soil C and nitrogen (N) contents. CDM was added to a mixture of perennial grasses at 22.4, 33.6 or 44.8 Mg ha− 1. A grass–legume treatment was established by interseeding alfalfa (Medicago sativa) into the grass mixture. A no-input control was sampled as a reference. Soils (0–5 and 5–15 cm) were sampled approximately 1.5 years after study implementation and wet sieved to obtain four aggregate size classes: large macroaggregates (> 2000 μm), small macroaggregates (250–2000 μm), microaggregates (53–250 μm) and silt and clay fraction (< 53 μm). Significant CDM influences were found in the 5–15 cm depth. The addition of 44.8 Mg CDM ha^-1 and alfalfa resulted in higher proportions of macroaggregates (> 250 μm) and mean weight diameter (MWD) than CDM added at 22.4 or 33.6 Mg ha^-1. Addition of CDM at low dose rate and alfalfa did not affect total soil or aggregate-associated organic C or N. However, addition of CDM at 44.8 Mg ha^-1 and alfalfa resulted in higher total soil microbial biomass C and N compared to CDM added at 22.4 and 33.6 Mg ha^-1. Large macroaggregates were found to be positively correlated with total soil microbial biomass C (R = 0.81,p = 0.002). In conclusion, compared to a low application rate of CDM, addition of a high application rate of CDM or alfalfa interseeding resulted in higher total soil microbial biomass C and N and macroaggregates, and these changes in microbial biomass and aggregation occurred very rapidly.