The study aimed to investigate the temporal changes of pH, sorption complex, and structure of soil organic matter through the forest soil profile under beech and spruce forests located in Jizera mountains (Czech Republic) and affected by natural and anthropogenic acidification. Soil samples were collected in four different years (2008, 2013, 2015, and 2020) in each horizon: fermented horizons (F), humified horizons (H), organo-mineral horizons (A), and subsurface mineral horizons (B) (cambic or spodic). The cation exchange capacity (CEC), base saturation (BS), exchangeable element contents, pH, and soil organic carbon content (SOC) were determined. The infrared soil spectra were used to calculate indices of potential wettability, aromaticity, and decomposition. Our results showed that most nutrients and aliphatic compounds were retained in the uppermost soil layers. The aromaticity of organic matter increased with depth, while polysaccharides, regarding the decomposition compound, disappeared through the soil horizons. In a long-term observation, SOC content had constantly increased under beech, while spruce remained stable in the organic horizons. Exchangeable element contents increased in each horizon, except for Al and Fe; their content quickly decreased in F horizons and slowly decreased in H horizon under both forest tree species, while the deeper horizons remained constant, but increased in A horizon under spruce. Continuously increasing base cations concentrations in sorption complex of both forest tree species during the study period revealed the effect of forest stand types on acid deposition reduction and mitigation. The temporal changes in CEC, BS, SOC, and soil wettability are more intensive in beech than in spruce forest floor.