Global agricultural intensifications are now considered as major factors for deterioration of biodiversity and hence ecosystem services. Among them, soil degradation has serious impacts on soil ecosystem functioning and also it is believed to be related to climate change by enhancing green house gas emissions from soil. Some Japanese farmers have successfully produced grains and crops adopting extensive management; no-tillage with weed green mulch, so called "natural farming". These fields provide us an opportunity to consider how soil management can improve soil biodiversity and hence ecosystem functioning of soils. We compared soil food webs under different land use history and management. The no-tillage weed green mulch management dramatically increased soil biodiversity and soil food web structure was well developed. At the same time, this management increased soil aggregate formation and soil carbon sequestration. Nutrient cycling was more efficient compared to the tillage and no-weed management. Increase in plant biodiversity (including weeds), and reduction of soil disturbance can create a soil providing high ecosystem functioning. Therefore recent advancement of ecological theory on both diversity-functioning and plant-soil interaction can help improvement of agricultural management.