The conversion of natural forest to agroforestry plantations and annual cropping systems alters the soil habitat and food resources for biota, including earthworms. Native earthworm species may disappear whereas exotic species with greater tolerance of disturbance and less niche specialisation may thrive. The objective of the study was to compare the earthworm diversity in managed forest and agroforestry systems, which were cultivated for mixed plantation and annual crop production on Mount Gede, Indonesia. All the habitats in the study area were impacted by humans. The forest habitat was a managed forest, with a permanent tree cover, whereas mixed plantation had a partial shrub cover. Meanwhile, homogenous plantation was cultivated with annual crops. Among 3787 individuals collected during July–October 2012, five Oriental earthworm species were identified in the soil communities of Mount Gede: Drawida nepalensis, Notoscolex javanica, Pheretima pura-group, Polypheretima moelleri, and Polypheretima sempolensis. Also, 18 species were found that are reported to be non-Oriental in origin. Anthropogenic disturbance of forests on Mount Gede, due to conversion into plantations, alters the earthworm environment by increasing soil water content, temperature and total phosphorous content, while decreasing organic carbon. N. javanica was the only native species to survive this deforestation, while the exotic Ocnerodrilus occidentalis and Pontoscolex corethrurus thrived, becoming the eudominant species. From the forest area to the mixed and homogenous plantations, the predicted decreasing diversity is evidenced by the lowering trend of Shannon’s diversity index. In conclusion, the land-use change into mixed plantations and annual croplands has reduced earthworm diversity in this region of Mount Gede, Indonesia.