Long-term mono-cropping often suppresses plant growth, but the mechanisms behind this are poorly understood. The key may lie in the soil surrounding the plants’ roots. This region, the rhizosphere, is filled with important microbes and the carbon-containing photosynthesis products, rhizodeposits, that plants exude from their roots. Rhizodeposits are part of the link between plants and their rhizosphere microbes. So, a team of researchers examined the interactions among rhizodeposits, rhizosphere microbes, and mono-cropping long-term. They found that years of mono-cropping led to a gradual decrease in carbon deposition and the chemical diversity of the rhizodeposits. These decreases were strongly correlated with decreases in the rhizosphere microbial diversity and metabolic functioning. Mono-cropping long-term also slowly led to a decrease in the abundance of plant-beneficial microbial groups. This study presents the first evidence of the mechanisms that underlie rhizosphere microbiome malfunction in mono-cropped systems and can be used to guide future research to improve the microbiome functioning of soil ecosystems.