In many studies, possibilities are being explored to adjust farm management to increase or maintain soil organic matter (SOM) contents in agricultural soils. Some options may be conflicting with efficient nutrient (N and P) management, i.e. management aiming at maximum conversion of imported nutrients into exported products (milk and meat in the case of dairy farms). This study explored long term effects of efficient nutrient management on SOM dynamics on an experimental dairy farm with three types of land use: permanent grassland, a 3 year grass–3 year arable crop rotation (ROTI), and a 3 year grass–5 year arable crop rotation (ROTII). The arable phase in the crop rotations consisted predominantly of maize. The experimental farm, called ‘De Marke’, is located on a Spodosol with an Anthropic Epipedon in the Netherlands. The study consisted of: i) trend analyses based on data of measured SOM mass percentage (SOM %) from 1989–2010, and ii) simulations of long term (50 years) SOM dynamics for four management alternatives. Three alternatives were related to manure digestion: no digestion; ‘mild anaerobic digestion’ (degrading 35% of organic matter) and; ‘strong digestion’ (degrading 70% of organic matter). The fourth management alternative was similar to the first (no digestion) but differed in that no catch crop was grown after maize. The trend analyses showed that SOM % of the 0–0.2 m layer was approximately stable under permanent grassland. In ROTI, SOM % decreased on average by 0.04 y− 1 and in ROTII by 0.03 y− 1. The decline did not slow down over time. SOM decline was more severe on plots with relatively high initial SOM %. Decomposition was described using a mono-component model with a time dependent relative decomposition rate. Decomposition rates in the rotations with arable crops were not higher than those for permanent grassland indicating that tillage did not affect decomposition rate and that SOM dynamics were dominated by the quantity and quality of the substrate input. Simulations indicated that in the long term, decline of SOM must be expected both under arable crop–grassland rotations and under permanent grassland, even in the case of permanent grassland receiving undigested manure. Our results further indicate that strong manure digestion puts pressure on future SOM levels suggesting a trade-off with bio-energy production, and that the contribution of a catch crop to long term SOM is marginal.