The shortage of data on nitrogen (N) air pollution in the Himalayas points to the opportunity to utilise lichens as bioindicators to understand ecological impacts. In this study, we examine the chemical variability of two widely occurring lichens (Usnea spp., Hypotrachyna spp.), considering physico-chemical properties and responses along two Nepalese forest transects representing N pollution gradients, along which we measured atmospheric ammonia (NH3) concentrations for the very first time in the region. The measured atmospheric NH3 concentrations ranged from 3.01–4.84 μg m–3 in the Kathmandu transect and 2.51–4.74 μg m–3 in the Annapurna Conservation Area (ACA) transect. We found higher thallus N, ammonium, and metal ion concentrations in both lichen species closer to local air pollution sources. The highest values were observed for lichens at the ACA transect, including for both physico-chemical parameters (electrical conductivity, chlorophyll content, chlorophyll fluorescence, phenolic content) and oxidative responses (radical scavenging, catalase activities), consistent with the higher levels of NH3 air pollution. We conclude that the atmospheric NH3 concentration has already exceeded the ecological threshold for effects on lichens in this region, highlighting a major risk of biodiversity loss. In the absence of large-scale air quality monitoring, the measured physico-chemical properties and oxidative responses can be used to inform the application of lichens as bioindicators of N and metal pollution. Further studies on other lichen species are recommended to better understand the functional biology explaining contrasting responses between lichen species of the Himalayan and (sub)tropical regions to strengthen their applicability for ecological monitoring.