Agriculture is the main source of atmospheric ammonia (NH3). Methodologies are needed to quantify national NH3 emissions. For European continental scale the EMEP emissions inventory with a 50 x 50 km(2) resolution is yearly available. However, current air quality models are often applied with higher spatial resolution, in order to obtain representative results, especially at urban and regional scales; therefore, a simple top-down approach based in the spatial interpolation of EMEP emissions is not sufficient. The aim of this work is the development and application of a mixed top-down and bottom-up methodology for high resolution emissions inventory for the agriculture sector, based on EMEP and other public data sources (E-PRTR inventory, statistical data, etc.) for Western Spain and Portugal. This new emission inventory was compared with EMEP and assessed using the WRF-CAMx air quality modelling system. Results highlighted the influence of the meteorology (high temperatures) and the magnitude of emissions on NH3 air quality concentrations. The higher resolution emissions lead to the highest maximum NH3 ground level concentrations, in specific locations. Copyright (C) 2016 Turkish National Committee for Air Pollution Research and Control. Production and hosting by Elsevier B. V. This is an open access article under the CC BY-NC-ND license