Plants interact strongly with soil and soil microbes to alter soil microbial communities. There is a knowledge gap on how plant species (and potentially their root exudate) influence soil microbial communities. To address this gap, we planted three crop species in three continuous planting cycles. We found that plant species alter fungal but not bacterial communities. Continuous planting changed both bacterial and fungal communities. This suggests that fungal communities strongly respond to different plant species, but the presence of plants shifts microbial communities over time. These results provide clues to manipulate plant-associated soil microbial communities to achieve targeted ecosystem services.