Biodiversity loss likely occurs in alpine ecosystems under climate warming. However, little is known about the effect of plant functional type loss on the litter decomposition rate and microbial community composition. To test whether single functional type loss has a significant impact on the litter decomposition and microbial community composition, we conducted a litterbag experiment by randomly removing a single functional type from the litter mixtures of six functional types (evergreen conifer, evergreen shrubs, deciduous shrub, graminoid, forb and fern). Moreover, incubation sites were established in two vegetation types with contrasting microclimatic conditions in an alpine timberline ecotone. Based on a two-year decomposition experiment, we found that random loss of the single plant functional type did not significantly affect the mass loss rates and microbial community biomass and structure in the two vegetation types. Moreover, most losses of single plant functional type affected the investigated mass loss rates and microbial parameters in an additive way. In contrast, there were significant effects of vegetation type on the microbial community composition, irrespective of plant functional type loss treatments. We conclude that mass loss rates and microbial parameters in litter mixtures are largely predictable from those in individual plant functional type in the alpine timberline ecotone. Our findings suggest that, under climate change scenarios, losses of single plant functional type possibly induced by upward shifts of alpine plants would alter the microbial community composition in litters only under the condition of changes in microclimatic factors (i.e., moisture and temperature), which would have a profound impact on alpine ecosystems.