Fungal non-pollen palynomorphs (fNPPs) are microscopic structures occurring in various sediments. In paleoecological studies, they can serve as reliable indicators of vegetation types, grazing activities, and human impact, enriching the interpretation of fossil data. This study explores the composition and taxonomic richness of fNPPs in 85 moss samples from a European lowland forest. We found rich fungal diversity, with 95 morphological types, predominantly saprotrophs, favoring specific substrates, like wood, decaying bark, herbaceous plant remains, litter, and freshwater habitats. Key taxa, such as type HdV-96A, and cf. Hypoxylon (EMA-24), were prevalent across different forest types, especially in deciduous forests. We identified two primary gradients of fNPP composition. The first axis delineated samples by taxonomic richness, Shannon index, and canopy openness, showing similarities among deciduous forests. The second axis ordered samples by the proportion of fNPPs, volume of stumps, coarse woody debris, and herbs pollen richness, highlighting their connections. Forest management intensity had minimal influence on fNPP composition, indicating consistent composition along both ordination axes. Forest type and herbs pollen richness, significantly affected the taxonomic richness and Shannon diversity of fNPPs. Deciduous forests exhibited higher fNPP richness, compared to coniferous forests, linked to increased herbs pollen richness. However, fNPPs decreased with increasing volume of stumps, coarse woody debris, and canopy openness, demonstrating the complexities of forest management’s influence on fungal diversity. This study pioneers fNPP investigation in an old-growth temperate forest ecosystem, emphasizing the interplay of forest characteristics, herbs diversity, and dead wood components in shaping their composition and richness. It also reveals differences in fNPP assemblages between deciduous and coniferous forests, underscoring the importance of forest type in shaping fungal diversity. These findings highlight the need for detailed studies on microhabitats, dead wood decomposition rates, and specific forest impacts to comprehensively understand forest ecosystem dynamics.