Headwater streams are fully linked to surrounding riparian vegetation through coarse and fine organic matter inputs. However, forestry operations in or close to riparian corridors, particularly in mountainous forested microcatchments, can alter both the organic matter dynamics and the composition, structure and function of stream macroinvertebrate assemblages. Although it is an issue of great concern elsewhere, in Andean headwater streams scarce information exist about this respect. By using a paired-catchment approach (thinned vs. unthinned) in two sets of selected evergreen and deciduous small streams in southern Chile (39°S), we evaluated the effects of forest harvest on seasonal and annual litterfall dynamics and the structural and functional attributes of macroinvertebrates between January 2008 and January 2009. Metrics used to assess changes included riparian litterfall input, invertebrate colonization and leaf decomposition of dominant plant species (evergreen: Laureliopsis philippiana, Myrceugenia planipes; deciduous: Nothofagus alpina), taxa richness, functional feeding group (FFG) composition, and their densities and biomasses for each stream. In both experimental trials, microcatchments registered significant differences in the seasonal litterfall input. The total organic matter input was as follows: Unthinned evergreen (UE) = 3699, thinned evergreen (TE) = 3249, unthinned deciduous (UD) = 3151, and thinned deciduous (TD) = 2981 kg ha−1y−1. Leaf dry mass losses were significantly higher during summer and spring for L. philippiana and during summer and autumn for N. alpina. These results were concomitant to decomposition rates and macroinvertebrate abundance during colonization of the leaf bags. Macroinvertebrate density and biomass were also contrasted; shredders were the dominant FFG and showed significant seasonal differences between microcatchments in both in-stream and leaf bag studies. There were generally no major changes in FFG composition or taxa richness, but differences were detected comparatively in the abundance or density of collectors and shredders. Our results suggest that forestry activities carried out on riparian vegetation of Andean headwater streams can affect the structural and functional role of plants and benthic invertebrates and nutrient fluxes downstream.