Arnica montana L. is a critically endangered and highly valued medicinal plant species in Europe. We show the inter-relationships between arnica and accompanying plant species, as well as soil factors, that promote the persistence of the studied forest arnica populations in terms of active protection of this species in the northeast region of Europe. The population characteristics and plant species composition were assessed during a field study. Additionally, soil samples were taken and analyzed to assess variation in soil conditions in the habitats of arnica populations. Correlations between population characteristics and soil properties were highlighted. The forest habitats of arnica presented in this study differ from those described in other European mountain and submountain areas. The sandy and very poor soils are characterized by a very low content of macro- and microelements, and a strong acid reaction. The positive correlation between population characteristics and Ca and K indicates an important role of these macroelements in flower head production. Acidity, K, Ca, the sum of exchangeable bases, and base saturation play crucial roles in the persistence of arnica populations in pine forests. The level of acidity and its consequences result from soil-forming processes and climatic conditions rather than air pollution. When planning active protection scenarios, special attention should be paid to the frequency and cover of Vaccinium myrtillus, which can act as a competitor in forest habitats. Assessment of soil conditions that favor the persistence of the studied arnica populations and species relationships is important for improving knowledge of the ecology of the species and for the active protection of endangered plant species.