• C. podzolicus Y3 eliminated OTA in PM medium and grape juice. • The intracellular substances of C. podzolicus Y3 strongly degraded OTA to OTα. • Intracellular substances eliminated OTA at different temperatures. • C. podzolicus Y3 simultaneous degraded CIT and OTA in NYDB medium. Ochratoxin A (OTA), a widespread mycotoxin contaminant in food and feed, threatens human and animal safety and causes significant economic losses. The aims of the present study were to investigate the elimination properties of Cryptococcus podzolicus Y3 on OTA and its co-degradation efficiency on citrinin (CIT) and OTA. C. podzolicus Y3 eliminated 100% OTA (1 μg/mL) in the PM media within 5 d and in grape juice media within 3 d by intracellular substances. The results of HPLC-FLD and LC-MS showed that OTA was efficiently eliminated into non-toxic ochratoxin α (OTα). The substances responsible for OTA degradation were thermostable and worked effectively at 4 °C and 28 °C, and intracellular proteins were participated in the elimination of OTA. In addition, the results showed that C. podzolicus Y3 degraded OTA and CIT together in NYDB media, although the degradation efficiency was lower than single mycotoxin degradation. Generally, our study highlighted that C. podzolicus Y3 could be a potential strain to eliminate OTA and CIT to secure food products and enhance food safety. [ABSTRACT FROM AUTHOR]