Biological pesticides are employed in organic agriculture to protect crops from pathogens and improve soil fertility. Substances used include by-products from local agricultural industry, such as olive mill wastewaters (OMWs). Until recently there has been little data concerning the effect of biological pesticides on soil microorganisms such as fungi 'Arbuscular mycorrhizal fungi' (AMF) and the wider fungal community. The Ecomycorrhiza project is, therefore, a timely investigation into effects of biological-based pesticides on non-target soil microbial communities. The AMF develop symbiotic relationships with most plants. The fungi can help improve the host plant's resistance to drought and minimise damage from pathogens. Selected AMF can be used in organic agriculture to benefit plant growth. The Ecomycorrhiza project has conducted a series of experiments to determine the status, diversity and function of AMF in vegetable cultivation on organic farms. Pure AMF cultures were isolated and their ability to colonise plants and promote plant growth and potassium (K) uptake on potted tomato and pepper plants was observed. Results from the pot experiments have been validated in field experiments, which enable these practices to be examined under realistic conditions. Findings from the Ecomycorrhiza project can help to improve the productivity of organic farms across Europe, which cannot use chemical fertilisers and pesticides to increase yields.