Substitution of mineral fertilizers with organic soil amendments is postulated to improve productivity‐relevant soil properties such as aggregation and organic matter (OM) content. However, there is a lack of studies analyzing the effects of biochar and biogas digestate versus mineral fertilizer on soil aggregation and OM dynamics under temperate field conditions. To address this research gap, a field experiment was sampled four years after establishment on a sandy Cambisol in Germany where mineral fertilizer or liquid biogas digestate was applied with or without 3 or 40 Mg biochar ha−1 (produced at 650°C). Soil samples were analyzed for soil organic carbon (SOC) content, pH, cation exchange capacity, bulk density, water‐holding capacity, microbial biomass, aggregate size class distribution, and the SOC content associated with these size classes. 40 Mg biochar ha−1 significantly increased SOC content in all fractions, especially free particulate OM and the 2–0.25 mm fraction. The yield of small macroaggregates (2–0.25 mm) was increased by biochar, but cation exchange capacity, water‐holding capacity, and pH were not consistently improved. Thus, high‐temperature biochar applied to a sandy soil under temperate conditions is primarily recommended to increase SOC content, which could contribute to climate change mitigation if this C remains sequestered over the long‐term. Fertilizer type did not significantly affect SOC content or other measured properties of the sandy Cambisol, suggesting that replacement of mineral fertilizer with digestate has a neutral effect on soil fertility. Co‐application of biochar with digestate provided no advantages for soil properties compared to co‐application with mineral fertilizer. Thus, independent utilization of these organic amendments is equally suitable.