Atmospheric deposition of nitrogen is responsible for widespread changes in the structure and function of sensitive seminatural ecosystems. The proposed reduction in emissions of nitrogenous pollutants in Europe under the Gothenburg Protocol raises the question of whether affected ecosystems have the potential to recover to their previous condition and, if so, over what timescale. Since 1998, we have monitored the response of a lowland heathland in southern England following the cessation of a long-term nitrogen addition experiment, and subsequent management, assessing changes in vegetation growth and chemistry, soil chemistry and the soil microbial community. Persistent effects of earlier nutrient loading on Calluna growth and phenology, and on the abundance of lichens, were apparent up to 8 years after nitrogen additions ceased, indicating the potential for long-term effects of modest nutrient loading (up to 15.4 kg N ha−1 yr−1, over 7 years) on heathland ecosystems. The size and activity of the soil microbial community was elevated in former N-treated plots, 6–8 years after additions ceased, suggesting a prolonged effect on the rate of nutrient cycling. Although habitat management in 1998 reduced nitrogen stores in plant biomass, effects on belowground nitrogen stores were small. Although some parameters (e.g. soil pH) recover pretreatment levels relatively rapidly, others (e.g. vegetation cover and microbial activity) respond much more slowly, indicating that the ecological effects of even small increases in nitrogen deposition will persist for many years after deposition inputs are reduced. Indeed, calculations suggest that the additional soil nitrogen storage associated with 7 years of experimental nitrogen inputs could sustain the observed effects on plant growth and phenology for several decades. Carry over effects on plant phenology and sensitivity to drought suggest that the persistence of vegetation responses to nitrogen deposition should be integrated into long-term assessments of the impact of global climate change on sensitive ecosystems.