The insect fauna of the Galápagos Islands is considered among the most pristine in the world and is well-studied in the preserved areas. However, introduced species are numerous and damaging, particularly in disturbed areas such as agricultural zones. In this study, we examined the arthropod diversity in two agricultural sites on Santa Cruz Island, Galápagos; a shaded mixed coffee plantation and an abandoned avocado plantation. We combined three sampling techniques to obtain a detailed picture of the invertebrate fauna in the leaf litter and in the lower arbustive zone. We then compared the two sites to assess the variation in arthropod fauna depending on the degree of disturbance. During the study, we collected individuals belonging to 96 taxa within the classes Arachnida, Insecta, Malacostracea and Diplopoda. More than half of the species were either endemic or native, but introduced species constituted the great majority (83.5%) of the sampled specimens. The invasive fire ant Solenopsis geminata Fabricius, 1804 was present in the majority of the samples and constituted almost half of the specimens collected. Although the faunal composition and species richness was similar in both sites, the evenness of species distribution was lower in the more disturbed avocado plantation. The same site hosted more S. geminata, fewer native species, and fewer predatory species than the shaded coffee plantation. We discuss these results by stressing the potential importance of non-intensive agricultural zones for the conservation of biodiversity and the possible impacts of S. geminata on native invertebrates in the Galápagos Islands.