Soil acidification and N saturation are considered to affect the decomposition of soil organic matter as well as growth and mortality of fine roots in many forest soils. Here we report from a field experiment where ‘clean rain’ has been applied to the soil for about 10 years under a roofed plot of a 71-year-old Norway spruce plantation at Solling, Central Germany. Reduced amounts of protons (−78%), sulphate (−53%), ammonium (−86%), and nitrate (−49%) were sprayed on the soil surface of the clean rain plot between 1992 and 2001. In an adjacent roofed control plot, throughfall was collected and immediately re-sprinkled below the roof construction without any chemical manipulation. One year before the clean rain treatment started, live and dead fine root masses (≤2 mm) were determined from undisturbed soil cores down to 40 cm mineral soil depth. Total live fine root mass was significantly lower in the clean rain plot than in the control plot. After the first sampling, the soil holes were refilled with quartz sand and repeatedly sampled in June 1992, June 1996, and October 2001. There were no differences in live and dead fine root masses between the plots in 1992 and 1996. In 2001, both live and dead fine root masses of the clean rain plot were about twice as high as in the control plot, indicating that fine root growth recovered in the mineral soil following 10 years of clean rain treatment. Moreover, the clean rain treatment significantly reduced the total N concentrations of live fine roots and 1-year-old needles. Our results suggest that the reduced N input promoted fine root growth to compensate N deficiency. Reduced Al concentration in soil solution may have contributed to the recovery of fine root growth, however, the toxicity of Al species is largely unknown. Mean annual soil respiration rate was 24% higher in the period from 2000 to 2001, indicating that the clean rain treatment increased respiration of roots and heterotrophic microorganisms within the rhizosphere. Laboratory incubation of samples from the organic horizon and the top mineral soil revealed no differences between the plots in the decay rate of soil organic matter. Our results suggest that strong reductions in atmospheric N deposition from about 30 to 10 kg N ha−1 yr−1 and decreasing acid stress can have beneficial effects on growth of fine roots in the mineral soil within a decade. We conclude that biological recovery under reduced atmospheric loads can affect the nutrient and carbon budget of spruce soils in the long run.