Reduced nutrient mineralization rates under minimum tillage are usually compensated by mineral fertilizer application. These cannot be applied in organic farming systems, however. We hypothesized that organic minimum tillage based on frequent cover cropping and application of dead mulch will improve soil fertility and can compensate for the potential negative effects of minimum tillage. Two long-term field experiments were set up in 2010 and 2011 comparing plough versus minimum tillage including application of transferred mulch. As second factor, the application of compost versus mineral potassium and phosphorus was compared. In 2019, soils were analyzed for soil pH, organic carbon, macro-, micronutrients, microbial biomass, microbial activity and total nematode abundance. In addition, performance of pea in the same soils was determined under greenhouse conditions. Across both experiments, macronutrients (+52%), micronutrients (+11%), microbial biomass (+51%), microbial activity (+86%), and bacterivorous nematodes (+112%) increased in minimum tillage compared with the plough-based system. In the greenhouse, pea biomass was 45% higher in the soil that had been subjected to minimum tillage compared to the plough. In conclusion, soil fertility can be improved in organic minimum tillage systems by intensive cover cropping and application of dead mulch to levels higher than in a plough-based system.