Expansion of agriculture is particularly worrying in tropical regions of the world, where native forests have been replaced by croplands and grasslands, with severe consequences for biodiversity conservation and ecosystem functioning. However, limited data exist on the effects of agriculture on the functioning of tropical streams. We conducted a leaf litter decomposition experiment in coarse- and fine-mesh litterbags using the three species of leaves (Eucalyptus globulus [non-native], Vernonia myriantha, and Syzygium cordatum [indigenous]) in three forested and agricultural streams to determine the effect of agriculture on instream leaf litter decomposition in headwater stream sites. We also examined the functional composition of macroinvertebrates in the streams through the contents of benthic kick samples. Agricultural streams had a less dense riparian canopy and smaller abundance of coarse organic particulate matter, and higher electric conductivity and suspended solids than forested streams. In terms of the effects of litter quality on decomposition rates, Vernonia had the fastest decomposition rates while Eucalyptus had the slowest in both forested and agricultural sites. Shredder invertebrates were less abundant in agricultural streams, and in both stream types, they were less diverse and abundant than other functional groups. Overall, leaf litter decomposition rates did not respond to agricultural land-use. The hypothesized negative effects of agriculture on organic matter processing were minimal and likely modulated by intact riparian zones along agricultural streams.