Aryl phosphorus flame retardants (aryl-PFRs), such as triphenyl phosphate (TPHP) and diphenyl phosphate (DPHP), are widely used worldwide. Understanding the fates of aryl-PFRs in vivo is crucial to assessing their toxicity and the risks they pose. Seven TPHP metabolites, including Phase I hydrolysis and hydroxylation and Phase II glucuronidation products, were identified in C57BL/6J male mice following subacute dietary exposure to aryl-PFRs (70 μg/kg body weight (bw)/day) for 7 days. TPHP was almost completely metabolized by mice (∼97%), with DPHP the major metabolite formed (34%−58%). In addition, mice were exposed to aryl-PFRs (7 μg/kg bw/day) for 12 weeks. Both TPHP and DPHP occurred at higher concentrations in the digestive tract (intestine and stomach), liver and heart. The total concentration of DPHP in all organs was 3.55-fold greater than that of TPHP. Recovery analysis showed that the rate of TPHP elimination from mouse organs reached 38%, while only 3%−5% of DPHP was removed, suggesting that the rates of degradation and elimination of DPHP were slower than TPHP and its bioaccumulation potential was higher. These results highlight the critical role of DPHP in the biotransformation, bioaccumulation, and bioelimination of TPHP, providing valuable insights into the fate of aryl-PFRs in vivo.