Summary Phosphorus (P) is crucial nutrient element for crop growth and development. However, the network pathway regulating homeostasis of phosphate (Pi) in crops has many molecular breeding unknowns. Here, we report that an auxin response factor, OsARF12, functions in Pi homeostasis. Measurement of element content, quantitative reverse transcription polymerase chain reaction analysis and acid phosphatases (APases) activity assay showed that the osarf12 mutant and osarf12/25 double mutant with P‐intoxicated phenotypes had higher P concentrations, up‐regulation of the Pi transporter encoding genes and increased APase activity under Pi‐sufficient/‐deficient (+Pi/−Pi, 0.32/0 mM NaH2PO4) conditions. Transcript analysis revealed that Pi‐responsive genes – Phosphate starvation (OsIPS)1 and OsIPS2, SYG1/Pho81/XPR1(OsSPX1), Sulfoquinovosyldiacylglycerol 2 (OsSQD2), R2R3 MYB transcription factor (OsMYB2P‐1) and Transport Inhibitor Response1 (OsTIR1) – were more abundant in the osarf12 and osarf12/25 mutants under +Pi/−Pi conditions. Knockout of OsARF12 also influenced the transcript abundances of the OsPHR2 gene and its downstream components, such as OsMiR399j, OsPHO2, OsMiR827, OsSPX‐MFS1 and OsSPX‐MFS2. Results from –Pi/1‐naphthylphthalamic acid (NPA) treatments, and auxin reporter DR5::GUS staining suggest that root system alteration and Pi‐induced auxin response were at least partially controlled by OsARF12. These findings enrich our understanding of the biological functions of OsARF12, which also acts in regulating Pi homeostasis.