In agro-ecosystems, fertilization practices are crucial for sustaining crop productivity. Here, based on a 50-year long-term experiment, we studied the influence of fertilization practices (inorganic and/or organic) and nitrogen (N) application rates on (i) soil physicochemical properties, (ii) microbial and earthworm communities and (iii) crop production. Our results showed that soil organic carbon content was increased by incorporation of crop residues (+2.45%) and farmyard manure application (+6.40%) in comparison to the use of mineral fertilizer alone. In contrast, soil carbon stock was not significantly affected by these fertilization practices. Overall, only farmyard manure application improved soil physicochemical properties compared to mineral fertilization alone. Soil microbial population was enhanced by the application of organic amendments as indicated by microbial biomass and phospholipid-derived fatty acids contents. The fertilization practices and the N application rates affected significantly both the biomass and composition of earthworm populations, especially the epigeic and endogeic species. Finally, farmyard manure application significantly increased crop yield (+3.5%) in comparison to mineral fertilization alone. Crop residue incorporation rendered variable but similar crop yields over the 50-year period. The results of this long-term experiment indicate that the use of organic amendments not only reduces the need for higher amount of mineral N fertilizer but also improves the soil biological properties with direct effects on crop yield. (C) 2016 Agroscope. Published by Elsevier B.V.