Plant root exudates can form organo-mineral associations (OMAs) through physico-chemical interactions with soil mineral surfaces but can disrupt existing OMAs by increasing microbial decomposition and dissolution of OMAs. The controls on these seemingly opposing processes are not well understood, nor are OMA chemical and spatial characteristics that may explain net soil organic matter (SOM) gain or loss at the root-soil interface termed the rhizosphere. By labeling maize plants with 13CO2, we found that exudates caused a net SOM gain in the rhizosphere’s clay size fraction which contained high-activity minerals. The OMAs formed on rhizosphere clay particles were linked to microbial metabolism of exudates and were more spatially and chemically heterogeneous than non-rhizosphere OMAs. In contrast, we found a net SOM loss in the rhizosphere’s silt size fraction which contained low-activity minerals and that dry soil conditions mitigated this rhizosphere SOM loss. Our findings show that root exudates can simultaneously form and disrupt OMAs, mediated by mineral composition and soil moisture.