Mountain regions harbour high biodiversity; however, in numerous areas, they are strongly degraded by human activity. Our study reconstructs the development of the submontane forest belt (400 and 650 m a.s.l.) in the Beskid Wyspowy Mountains (Western Carpathians, Central Europe) affected by climate, humans, fire, and parasitic fungi during the Holocene. This forest belt is considered the most transformed by the human in the Carpathian region. Our multi-proxy study included analyses of pollen, non-pollen palynomorphs (NPPs), plant macrofossils, micro- and macrocharcoal (size fraction >100 µm, analysed in contiguous sampling), geochemical, and sedimentological markers. The results revealed that Picea abies dominated on the fen subjected to study at ca. 8510–5010 cal. BP. Tilia cordata was a substantial component of the submontane forest between ca. 8510 and 2970 cal. BP and it survived a probable Kretzschmaria deusta outbreak, as well as a period of increased fire activity (ca. 6000 cal. BP). The final retreat of forests with a substantial contribution of Tilia was induced by the expansion of Abies alba, Fagus sylvatica, and partly Carpinus betulus and was preceded by the period of increased fire activity and erosion. From ca. 900 cal. BP human-induced deforestations and agricultural and pastoral activity increased. The modern presence of woodlands with Pinus sylvestris and Larix decidua, in the submontane zone in the Beskid Wyspowy Mountains, is a result of sub-recent anthropogenic afforestation on overgrazed areas. The example of the Zbludza site reveals that changes related to fire and pathogen infections, if they have low magnitudes and new competitive taxa are absent, may be reversible in a forest composed of fire-intolerant tree taxa as Tilia. Nonetheless, the widespread submontane ecosystem degradation and the introduction of alien species hamper the regeneration of forest vegetation typical of the submontane zone.