Soil acidification has constituted an important ecological threat to forests in Central Europe since the 1950s. In areas that are sensitive to acid pollution, where the soil buffering capacity is naturally low, tree species can significantly modulate the extent of soil acidification by affecting throughfall deposition and the composition of litter. A principal difference can be expected between coniferous and broadleaf tree species. The aim of our study was to compare long-term trends in element cycling in two stands representing the main types of forest ecosystem in the region (Picea abies vs. Fagus sylvatica). In the period of 2005–2017, we continually measured element concentrations and fluxes in bulk precipitation, throughfall precipitation, and soil leachates. A continuous decline of acid deposition was detected in both bulk precipitation and throughfall. Declining deposition of S and N in both forests has led to the recovery of soil solution chemistry in the mineral soil, manifested by rising pH from 4.25 to 4.47 under spruce and from 4.42 to 4.69 in the beech stand. However, soil water in the spruce stand was more acidic, with higher concentrations of SO42− and Al when compared to the beech stand. While the acidity of soil leachates from organic horizons was driven mainly by organic anions, in lower mineral horizons it was controlled by inorganic acid anions. NO3− concentrations in deeper horizons of the spruce stand have diminished since 2006; however, in the beech plot, episodically elevated NO3− concentrations in mineral horizons are a sign of seasonal processes and of nearby perturbations. Higher output of S when compared to the input of the same element indicates slow S resorption, delaying the recovery of soil chemistry. Our results indicate that, although forest ecosystems are recovering from acidification, soil S retention and the ability to immobilize N is affected by the dominant tree species.