With inevitable link between ecosystem function (EF), ecosystem services (ES) and agricultural productivity, there is a need for quantification and valuation of EF and ES in agro-ecosystems. Management practices have significant effects on soil organic matter (SOM), affecting productivity, EF and ES provision. The objective was to quantify two EF: soil water storage and nitrogen mineralization and three ES: food and fodder production and carbon sequestration, in a conventional winter wheat production system at 2.6% SOM compared to 50% lower (1.3%) and 50% higher (3.9%) SOM in Denmark by DAISY model. At 2.6% SOM, the food and fodder production was 6.49 and 6.86 t ha−1 year−1 respectively whereas carbon sequestration and soil water storage was 9.73 t ha−1 year−1 and 684 mm ha−1 year−1 respectively and nitrogen mineralisation was 83.58 kg ha−1 year−1. At 2.6% SOM, the two EF and three ES values were US$ 177 and US$ 2542 ha−1 year−1 respectively equivalent to US$ 96 and US$1370 million year−1 respectively in Denmark. The EF and ES quantities and values were positively correlated with SOM content. Hence, the quantification and valuation of EF and ES provides an empirical tool for optimising the EF and ES provision for agricultural productivity.