This work aimed for the first time to provide detailed insights into thymol and trans-cinnamaldehyde's mechanisms of action on the food-spoilage yeast Zygosaccharomyces rouxii and offers evidence in favor of the activation of an apoptosis-like phenotype. The action mechanisms of thymol and transcinnamaldehyde were investigated by the measurement of a series of typical apoptotic features using flow cytometer or microplate reader. Moreover, quantitative reverse transcription PCR (QRT-PCR) was performed to investigate the effects of thymol and trans-cinnamaldehyde on the transcription of key regulators of apoptosis in Z. rouxii. The results indicated that the treatment of Z. rouxii with thymol or trans-cinnamaldehyde (minimum inhibitory and subinhibitory concentrations) triggered reactive oxygen species (ROS) accumulation, elevated intracellular Ca 2+ level, and depolarized mitochondrial membrane potential (MMP) coupled with hallmarks of apoptosis including mitochondrial cytochrome c (cyt c) release, metacaspase activation, phosphatidylserine (PS) exposure, and DNA fragmentation. Moreover, thymol or trans-cinnamaldehyde treatment upregulated the transcription of proapoptotic regulators including Yca1, Dnm1, Nuc1, Ndi1, and Mmi1 and downregulated the transcription of antiapoptotic regulators of Fis1 and Cdc48, further confirming the apoptosis induced by thymol and trans-cinnamaldehyde in Z. rouxii. In summary, thymol and transcinnamaldehyde probably induced apoptosis through a metacaspase-dependent mitochondrial pathway in Z. roxuii. These findings provide theoretical support for the development of safe and efficient agents used in food preservation.