A history of excessive fertilization in Flanders’ intensively managed agriculture, causes severe nitrogen (N) and phosphorus (P) losses to water bodies. The local government took action from the 1990s onwards, by introducing restrictions to N and P fertilizer use. These restrictions also limit the supply of organic matter to the soil, while the soil organic matter level of many agricultural soils is suboptimal in Flanders. Moreover, P is an immobile nutrient and P fertilizer efficiency is low as only a minor part is directly available for plant up-take. We compared the effect of three compost types, cattle slurry, farmyard manure and mineral fertilizers on crop yield, soil organic carbon content, P availability, P export and P leaching in a long-term field experiment with arable, vegetable and fodder crops. Organic fertilizer doses were calculated every year for equal C input, and were always combined with mineral NPK. Total N supply fulfilled the demands of the crops and total P input was set equal to 100kg P2O5/ha.yr. As expected, farmyard manure and compost are the best options to enhance the total organic carbon level of the soil. Cattle slurry and mineral fertilizers tended to produce lower crop yields. P plant availability increased in the farmyard manure treatment, but did not lead to extra P export. Probably the soil delivers already sufficient P to the crops, and increasing P availability is not necessary. In a column leaching experiment in unsaturated conditions based on soil samples of this field experiment, increased potential P leaching was observed in the farmyard manure treatment. We conclude that evolution in soil organic carbon level and P plant availability, but also potential P leaching is dependent on organic fertilizer type. Compost shows to be an interesting product, as it can gradually increase TOC level, without increasing potential P leaching losses. Moreover compost has a positive effect on crop yield.