The effect of two types of organic amendment (manure and straw incorporation) and various doses (0–200 kg N*ha−1) of mineral N fertilization on microbial biomass C (MBC), aggregate stability (AS), soil organic C (SOC) and grain yield were investigated in an IOSDV long-term fertilization experiment (Keszthely, Hungary). This study was conducted during years 2015–2016 in a sandy loam Ramann-type brown forest soil (Eutric Cambisol according to WRB). Organic amendments had a significant effect on AS, MBC and SOC, increased their values compared to the unamended control. The organic amendments showed different effects on AS and MBC. AS was increased the most by straw incorporation and MBC by manure application. The magnitude of temporal variability of AS and MBC differed. Presumably, the different effects of organic amendments and the different degrees of temporal variability explain why there was only a weak (0.173) correlation between AS and MBC. AS did not correlate with SOC or grain yield. MBC correlated (0.339) with SOC but not with the grain yield. The N fertilizer dose did not have a significant effect on AS and MBC, but had a significant effect on SOC and grain yield.