Forest change occurs worldwide, especially on islands where space is a limiting factor for human activities. The replacement of diverse native forests by tree monocultures and subsequent changes in litter input characteristics can have strong effects on stream communities and processes. Aquatic decomposers and litter decomposition can be particularly sensitive to forest change due to their dependence on terrestrial litter supply and on litter characteristics. However, studies addressing the effects of forest changes, and conifer plantations in particular, on stream litter decomposition and associated decomposers are scarce. Here, we assessed the effects of the replacement of native laurel forests in São Miguel island, Azores archipelago, by commercial conifer plantations (Cryptomeria japonica (L. f.) D. Don) on litter decomposition and associated fungal decomposers. Leaves of the native broadleaf tree Ilex perado Aiton and conifer needles were enclosed in mesh bags and incubated in three streams flowing through conifer plantations and three streams flowing through native laurel forests in winter 2015 for determination of litter decomposition rates, and aquatic hyphomycete community structure and reproductive activity (one stream per type). Aquatic hyphomycete communities’ structure strongly differed between native and conifer streams as a result from differences in the total number of species recorded (higher in the native stream), species identity (only 10 species, out of 26, were common to both streams) and species evenness (higher in the native stream). These differences in communities between streams likely result from changes in litter inputs characteristics between native and conifer streams and from aquatic hyphomycetes having substrate preferences. Differences in aquatic hyphomycete communities were not accompanied by differences in litter decomposition rates between native and conifer streams, which likely results from functional redundancy between decomposer communities and suggests that community structure and function may not always be tightly coupled. Litter decomposition rates did not differ between native and conifer species because I. perado leaves were tough and had a tick waxy cuticle, which may have limited microbial development, as for the conifer needles. Thus, the replacement of native laurel forests by conifer plantations did not affect litter decomposition in Azorean streams likely because litter is recalcitrant and decomposition is driven by microbes. However, changes in aquatic hyphomycete communities arriving from forest change may have unpredictable effects in case of additional environmental change. Hence, to prevent unwanted effects of changes in microbial communities, a riparian buffer of native vegetation should be maintained in conifer plantations.