Although islands as natural laboratories have held the attention of scientists for centuries, they continue to offer new study questions, especially in the context of the current biodiversity crisis. To date, habitat diversity on islands and spatial configuration of archipelagos have received less attention than classical island area and isolation. Moreover, in the field where experiments are impossible, correlative methods have dominated, despite the call for more mechanistic approaches. We developed an agent‐based computer simulation to study the effect of habitat diversity and archipelago configuration on plant species richness and composition in five archipelagos worldwide (Hawaii, Galapagos, Canary Islands, Cape Verde and Azores) and compared simulated diversity patterns to the empirical data. Habitat diversity proved to be an important factor to achieve realistic simulation results in all five archipelagos, whereas spatial structure of archipelagos was important in more elongated archipelagos. In most cases, simulation results correlate stronger with spermatophyte than with pteridophyte data, which we suggest can be attributed to the different dispersal and evolution rates of the two species groups. Correlation strength between simulated and observed diversity also varied among archipelagos, suggesting that geological and biogeographic histories of archipelagos have affected the species richness and composition on the islands. Our study demonstrates that a relatively simple computer simulation involving just a few essential processes can largely emulate patterns of archipelagic species richness and composition and serve as a powerful additional method to complement empirical approaches.