Abstract. A system for fast ammonia (NH₃) measurements with chemical ionisation mass spectrometry (CIMS) based on a commercial Proton Transfer Reaction-Mass Spectrometer (PTR-MS) is presented. It uses electron transfer reaction as ionisation pathway and features a drift tube of polyetheretherketone (PEEK) and silica-coated steel. Heating the instrumental inlet and the drift tube to 180 °C enabled an effective time resolution of ~1 s and made it possible to apply the instrument for eddy covariance (EC) measurements. EC fluxes of NH₃ were measured over two agricultural fields in Oensingen, Switzerland, following fertilisations with cattle slurry. Air was aspirated close to a sonic anemometer at a flow of 100 STP L min⁻¹ and was directed through a 23 m long 1/2" PFA tube heated to 150 °C to an air-conditioned trailer where the gas was sub-sampled from the large bypass stream. This setup minimised damping of fast NH₃ concentration changes between the sampling point and the actual measurement. High-frequency attenuation loss of the NH₃ fluxes of 20 to 40% was quantified and corrected for using an empirical ogive method. The instrumental NH₃ background signal showed a minor interference with H₂O which was characterised in the laboratory. The resulting correction of the NH₃ flux after slurry spreading was less than 1‰. The flux detection limit of the EC system was about 5 ng m⁻² s⁻¹ while the accuracy of individual flux measurements was estimated 16% for the high-flux regime during these experiments. The NH₃ emissions after broad spreading of the slurry showed an initial maximum of 150 μg m⁻² s⁻¹ with a fast decline in the following hours.