The understanding of biochemical feedback mechanisms in the climate system is lacking knowledge in relation to bi-directional ammonia (NH3) exchange between natural ecosystems and the atmosphere. We therefore study the atmospheric NH3 fluxes during a 25-day period during autumn 2010 (21 October to 15 November) for the Danish beech forest Lille Bøgeskov to address the hypothesis that NH3 emissions occur from deciduous forests in relation to leaf fall. This is accomplished by using observations of vegetation status, NH3 fluxes and model calculations. Vegetation status was observed using plant area index (PAI) and leaf area index (LAI). NH3 fluxes were measured using the relaxed eddy accumulation (REA) method. The REA-based NH3 concentrations were compared to NH3 denuder measurements. Model calculations of the atmospheric NH3 concentration were obtained with the Danish Ammonia MOdelling System (DAMOS). The relative contribution from the forest components to the atmospheric NH3 flux was assessed using a simple two-layer bi-directional canopy compensation point model. A total of 57.7% of the fluxes measured showed emission and 19.5% showed deposition. A clear tendency of the flux going from deposition of −0.25 ± 0.30 μg NH3-N m−2 s−1 to emission of up to 0.67 ± 0.28 μg NH3-N m−2 s−1 throughout the measurement period was found. In the leaf fall period (23 October to 8 November), an increase in the atmospheric NH3 concentrations was related to the increasing forest NH3 flux. Following leaf fall, the magnitude and temporal structure of the measured NH3 emission fluxes could be adequately reproduced with the bi-directional resistance model; it suggested the forest ground layer (soil and litter) to be the main contributing component to the NH3 emissions. The modelled concentration from DAMOS fits well the measured concentrations before leaf fall, but during and after leaf fall, the modelled concentrations are too low. The results indicate that the missing contribution to atmospheric NH3 concentration from vegetative surfaces related to leaf fall are of a relatively large magnitude. We therefore conclude that emissions from deciduous forests are important to include in model calculations of atmospheric NH3 for forest ecosystems. Finally, diurnal variations in the measured NH3 concentrations were related to meteorological conditions, forest phenology and the spatial distribution of local anthropogenic NH3 sources. This suggests that an accurate description of ammonia fluxes over forest ecosystems requires a dynamic description of atmospheric and vegetation processes.