The aim of this study was to compare the influence of two different long-term organic fertilization regimes at an arable site on a nutrient-poor, sandy soil with respect to soil microbial biomass contents and microbial activities. The investigation was performed on a long-term experimental arable field site, located in the semi-continental climate of Central Europe (IOSDV, Berlin–Dahlem, Germany). Soil microbial biomass and dehydrogenase activity were most clearly increased by combined straw and green manure treatment. In comparison, farmyard manure had a weaker effect, explained by less frequent applications and different quality of organic materials incorporated into soil. The mineral N-fertilization did not significantly effect microbial biomass content or dehydrogenase activity of the soil under study. The cellulase activity was increased markedly by straw and green manure treatment, but was increased only slightly by mineral fertilization. Organic manuring with plant residues had a stronger impact on soil microbial activity as compared to different soil sampling dates. We conclude that soil microbial activity was governed most clearly by the fertilization regime under the conditions of the investigated field experiment. Furthermore, manuring with plant residues has the most beneficial effects on soil quality among the investigated types of fertilization.