Farmers have to combine several measures to balance carbon contents in the top soil to preserve soil quality but potentially increasing the risk for N and P losses by leaching. We studied the effect of a combination of several measures on topsoil C content, nutrient leaching and soil quality in a multi-year field trial. Soil quality was defined as the result of the interaction between chemical, physical and biological soil characteristics, and included an assessment of disease suppressiveness as well. Initially, the soil had a suboptimal C content (i.e. 0.81%). Soil organic carbon (SOC) levels were maintained and slightly increased by applying slurry and good agricultural practices such as the use of cover crops and the incorporation of cereal straw (on average +0.04 percentage point). Only with a yearly extra plant-based farm compost amendment SOC levels were substantially increased after a period of four years (on average +0.17 percentage point). This application of 8.3 Mg C ha−1 also improved chemical, physical and biological soil quality. Our research demonstrates that farmers can use compost, for at least 4 years, on top of cattle or pig slurry application to soils with suboptimal C levels to increase C content in the top soil, without inducing higher N and P leaching. Repeated compost application increased the microbial biomass (measured by means of PLFA) and disease suppressiveness against Botrytis cinerea on lettuce. There was no effect on the abundance of the plant-parasitic nematode Pratylenchus penetrans in the soil, nor on disease severity caused by Dickeya solani, Streptomyces scabies and Rhizoctonia solani after a potato cropping. Differences between tillage practices were most obvious in the 0–10 cm soil layer as non-inversion tillage (compared to ploughing) resulted in an increase in SOC, Total N, hot-water extractable C and P, plant-available P and K, aggregate stability, earthworm abundance and bacterial and fungal populations in this layer.