Purpose The objective of this study was to determine the impact of restoration processes on the selected soil properties and organic matter transformation of mountain fens under the Caltho-Alnetum community in the Babiogórski National Park in Outer Flysch Carpathians. Materials and methods Restoration processes were conducted on three degraded mountain fens in the Babiogórski National Park in Outer Flysch Carpathians, Poland. The degradation degree of soils was the criterion for the selection of habitats for further studies. To determine the influence of restoration processes on mountain fen soil properties and organic matter transformation, samples were collected in 2011 and 2013. The soil samples were assayed for pH, base cation concentration, hydrolytic acidity, organic carbon and total nitrogen content, total exchangeable base cation concentration, cation exchange capacity, and base saturation. Organic matter fractions were extracted by IHSS method. Quantitative and qualitative study of organic matter was based on fraction composition analysis and the ratio of humic acid carbon to fulvic acid carbon. The research results were statistically verified. Results and discussion Based on morphological and chemical properties, the studied mountain fen soils can be classified as Sapric Dranic Eutric Histosols and Sapric Dranic Dystric Histosols according to WRB guidelines (2015). Before restoration processes, the mountain fen soils subjected to a different water regime showed various contents of total nitrogen and organic carbon. The decreasing of the groundwater level was reflected in pH, calcium ion content, exchangeable base cation concentration, and base saturation. The increase of the groundwater level had influence on chemical properties of mountain fen soils such as pH, total exchangeable base cation concentration, hydrolytic acidity, cation exchange capacity, and base saturation. Three-year restoration processes did not cause significant changes in the composition of humic substance fractions. Conclusions Mountain fens under Caltho-Alnetum community are priority habitats in Babiogórski National Park in Outer Flysch Carpathians, Poland. These habitats responded to restoration processes in varying degrees depending on the extent of their degradation. The least degraded mountain fen was characterized by a short response time on the restoration processes. The reaction of higher degraded habitats was weaker.