Background <p>As an important driver of plant performance, the rhizobiome is altered throughout plant maturation and agricultural management, such as diversified crop rotation systems. However, a comprehensive understanding of the temporal changes in the rhizobiome (bacteria, fungi, and protists) community composition and functioning during plant maturation remains little known, especially in response to different rotation systems.</p> Results <p>We collected rhizobiome samples in four developmental stages of wheat across four different rotation systems in a long-term field experiment. Across rotation systems, wheat maturation increased bacterial and fungal diversity, and changed their community compositions, while protist communities remained unaffected. Subsequently, we validated the functioning of rhizobiomes specific to distinct rotation systems and wheat developmental stages in a greenhouse experiment. The rhizobiome in the jointing stage enhanced maize height, which was best explained by a higher relative abundance of rhizobiome predators (predominantly protists) irrespective of rotation systems. We also found a positive correlation of rhizobiome predators with the maize shoot/root biomass ratio in our greenhouse experiment, suggesting that rhizobiome predators mobilize nutrients to favour plant shoot growth.</p> Conclusions <p>We conclude that a tight plant-rhizobiome feedback loop is, independent of agricultural management, internally fostered by rhizobiome predators and wheat maturation. Our results call for studies that aim to elucidate the potential drivers underlying plant growth-induced changes in the rhizobiome to develop targeted manipulations of plant growth promoting rhizobiomes.</p>