The intensive management of cropland refers to a reduction in habitat complexity (i.e., shade tree cover, tree species richness, crop species richness) to gain more profits. This usually entails a decrease in biodiversity, but agroforestry systems have been shown to provide a solution to the need for profits while maintaining biodiversity and ecosystem services. Invertebrates are important bioindicators since they are not just affected by a decrease in habitat complexity; they are also key for the maintenance of ecosystems given their ecological roles. We aimed to understand how agricultural intensification impacted invertebrate abundance and richness in an agroforestry system in Bali, Indonesia. We set up 53 × 25 m2 plots and collected data via pitfall and pan traps. We linked those data to vegetation data (canopy cover, tree species richness, crop species richness), habitat type (rustic vs. polyculture), and productivity. Overall, we found that the abundance and richness of invertebrate taxa were positively influenced by increasing canopy cover and crop and tree species richness. This supports the habitat heterogeneity hypothesis, which indicates that increased habitat complexity promotes higher invertebrate species richness and abundance. The abundance and richness of certain invertebrate taxa, including agents of biocontrol, were shown to increase in plots with higher yields, thus solidifying the important role of invertebrate communities in the provision of ecosystem services. Harvesting crops from complex agroforestry systems ensures a sustainable income for local communities as well as habitats for invertebrates.