The invention relates to a process and a plant for implementing the method to reduce nitrogen from organic substrates with a high nitrogen content, such as the manure produced by laying hens or other poultry, by means of a thermal pre-treatment in two stages that favours the transformation of organic nitrogen content in organic substrates with high concentrations of total nitrogen into ammonia for its subsequent removal. This procedure implements a sequence that is composed of a heating to temperatures typical of the hydrolysis/acidogenesis followed by a second step of heat treatment, with raising the temperature up to temperatures between 65 and 95°C (Fig. 1).