Ochratoxin A (OTA) is one of the most common and deleterious mycotoxins found in food and feedstuffs worldwide; however, Apiotrichum mycotoxinivorans can detoxify OTA. Our results show that A. mycotoxinivorans GUM1709 efficiently degraded OTA, but it caused the accumulation of intracellular reactive oxygen species. The main aim of this study was to identify potential OTA-detoxifying enzymes and to explore the effects of OTA on A. mycotoxinivorans GMU1709. RNA-seq data revealed that 1643 and 1980 genes were significantly upregulated and downregulated, respectively, after OTA exposure. Functional enrichment analyses indicated that OTA exposure enhanced defense capability, protein transport, endocytosis, and energy metabolism; caused ribosomal stress; suppressed DNA replication and transcription; inhibited cell growth and division; and promoted cell death. The integration of secretome, gene expression, and molecular docking analyses revealed that two carboxypeptidase homologues (members of the metallocarboxypeptidase family) were most likely responsible for the detoxification of both extracellular and intracellular OTA. Superoxide dismutase and catalase were the main genes activated in response to oxidative stress. In addition, analysis of key genes associated with cell division and apoptosis showed that OTA exposure inhibited mitosis and promoted cell death. This study revealed the possible OTA response and detoxification mechanisms in A. mycotoxinivorans. Display omitted •A. mycotoxinivorans GMU1709 efficiently degraded ochratoxin A (OTA).•OTA exposure induced metabolic pathways and genes involved in stress response.•CPA and CPY potentially contributed to OTA degradation in GMU1709.•Exposure to OTA may activate the antioxidant system of GMU1709.•OTA exposure inhibited the growth of GMU1709 and promoted its apoptosis.