The deposition of acidifying nitrogen and sulphur compounds from agriculture and fossil fuel combustion has drastically altered the chemical balance of forest soils in many regions of the world, leading to soil acidification with negative impacts on nutrient availability and thus also on tree vitality. The change of nutrient concentrations in the soil solution can be assessed by long-term investigations, however meaningful indicators, reflecting environmental changes, are needed to compare the current nutrient status with past values. We used dendrochemical indicators in stem wood of different tree species to access the impact of acidifying depositions on soil quality and tree nutrition. We selected 328 stem wood samples from 96 trees of Norway spruce (Picea abies), European beech (Fagus sylvatica), Sessile oak (Quercus petrea) and English oak (Quercus robur) from 22 forest sites, which are part of the long-term Intercantonal Forest Observation Program in Switzerland. Four time periods of 20 years were defined according to the emissions of air pollutants between 1910 and 2017. Our results showed a trend of increasing Al concentrations in tree rings of spruce peaking in the most recent time period (2000–2017). Mn and Ca concentrations in spruce and beech wood have decreased significantly throughout the time period 1910–2017. These dendrochemical indicators depended on the soil pH, with higher Al and lower Mn and Ca concentrations for soils with a low pH (pH<4.2). In oak trees the observed dendrochemical changes are confounded with dendrochemical differences between heartwood and sapwood. K and Mg showed inconsistent patterns in all three tree species, which are probably caused by translocation within the stem discs. With the use of piecewise structural equation models (SEM) we highlighted the direct and indirect influences of N deposition on element concentrations in stem wood. The data suggest a relation between increased N deposition and lower base saturation values in the forest soils for all three tree species, which were linked to higher Al concentrations in spruce and lower Mn concentrations in spruce and beech. The relation between Al concentrations in tree rings of Norway spruce and measured base saturation was used to reconstruct past soil base saturation values. It revealed a progressive soil acidification in the long-term forest observation sites. These reconstructed base saturation values were further used to validate modelled values from dynamic biogeochemical models such as SAFE/ForSAFE. This comparison pointed out possible shortcomings such as the lack of organic complexation in those models. Taken together, our analyses showed that element concentrations of Al, Mn, Ca in Norway spruce and European beech stem wood were suitable dendrochemical indicators of environmental change due to soil acidification, as they reflect both direct and indirect effects of air pollutants and chemical soil properties.