Scientific expertise of João Coutinho deals mainly with soil fertility, nutrient management and environmental impacts of mineral and organic fertilizers. Soil acidity and aluminum toxicity was the theme of his PhD. Since that, his research is focused in nutrient cycling in soils (carbon, nitrogen and phosphorus) with or without the application of organic residues to soils, emission of GHG to atmosphere, soil biochemical indicators of soil quality (soil microbial biomass, enzymatic activity, soil respiration and mineralisation and nitrification potentials) and organic farming in microcosms and field scale experiments. Simultaneously, and since 1979, he is responsible of the Soil and Plant Analysis Laboratory of UTAD, where several PhD and Master students develop thesis carried out under the referred domains.
In 2017 was appointed the Portuguese representative for the Global Soil Laboratory Network, launched by FAO through the Global Soil Partnership.