Microbially-mediated leaf litter decomposition is a critical ecosystem function in running waters within forested areas, which can be affected by fungicides. However, fungicide effects on leaf litter decomposition have been investigated almost exclusively with black alder leaves, a leaf species with traits favourable to consumers (i.e., low recalcitrance and high nutrient content). At the same time, little is known about fungicide effects on microbial colonisation and decomposition of other leaf species with less favourable traits. In this 21 day lasting study, we explore the effects of increasing fungicide sum concentrations (0–3000 µg/L) on microbial colonisation and decomposition of three leaf species (black alder, Norway maple and European beech) differing in terms of recalcitrance and nutrient content. Leaf litter decomposition rate, leaf-associated fungal biomass and bacterial density were quantified to observe potential effects at the functional level. Beech, as the species with the least favourable leaf traits, showed a substantially lower decomposition rate (50%) in absence of fungicides than alder and maple. In the presence of high fungicide concentrations (300–3000 µg/L), beech showed a concentration-related decrease not only in microbial leaf litter decomposition but also fungal biomass. This suggests that favourable traits of leaf litter (as for alder and maple) enable leaf-associated microorganisms to acquire leaf-bound energy more easily to withstand potential effects induced by fungicide exposure. Our results indicate the need to deepen our understanding on how leaf species’ traits interact with the impact of chemical stressors on the leaf decomposition activity of microbial communities.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00128-023-03728-2.