Fluoridated apatite (FAP) is the dominant P source for ecosystems. However, the bioweathering of FAP is still not fully elucidated. In this study, phosphate-solubilizing fungus (<em>Aspergillus niger</em>) was firstly incubated in soil to examine the weathering of FAP, on both cross and longitudinal sections. It showed that the fungus induced more pronounced erosion channels on the cross sections in a P-deficient soil. We therefore aimed to disentangle the relative contributions of biological (phosphate-solubilizing fungus) and abiotic factors (CO<sub>2</sub> and crystal face orientation) to the observed weathering contrasts. To further investigate the weathering contrasts on different sections of FAP, incubation was conducted in a culture medium. Fungal colonization on the cross section of FAP resulted in deeper P depletion zones and enriched secondary minerals (primarily calcium oxalate) than those on the longitudinal section. Additionally, elevated CO<sub>2</sub> (10 %) significantly accelerated the weathering of FAP on the cross section, which was confirmed by its enhanced surface roughness, further promoted fungal colonization and subsequent bioweathering for FAP. Synergistic interactions between fungi and elevated CO<sub>2</sub> accelerate phosphate mineral weathering, providing a new insight on P cycling in soil microenvironments such as the rhizosphere.