The intestinal tract microbiota influences many aspects of the dietary components on colon health and during enteric infections, thus, playing a pivotal role in the colon health. Therefore, the eugenol (EU) nano-emulsion effective concentration reported in our previous study against cancer cells should be explored for safety against beneficial microbes. We evaluated the sensitivity of Bifidobacterium breve and B. adolescentis against EU-loaded nano-emulsions at 0, 300, 600 and 900 µm, which were effective against colon and liver cancer cells. Both B. breve and B. adolescentis showed comparable growth ranges to the control group at 300 and 600 µm, as evident from the plate count experimental results. However, at 900 µm, a slight growth variation was revealed with respect to the control group. The real-time inhibition determination through flow cytometry showed B. breve viable, sublethal cells (99.49 and 0.51%) and B. adolescentis (95.59 and 0.15%) at 900 µm, suggesting slight inhibition even at the highest tested concentration. Flow cytometry proved to be a suitable quantitative approach that has revealed separate live, dead, and susceptible cells upon treatment with EU nano-emulsion against Escherichia coli. Similarly, in the case of B. breve and B. adolescentis, the cells showed only live cells that qualitatively suggest EU nano-emulsion safety. To judge the viability of these sublethal populations of B. breve and B. adolescentis, Fourier transforms infrared spectroscopy was carried out, revealing no peak shift for proteins, lipids, DNA and carbohydrates at 900 µm EU nano-emulsion compared to the control. On the other hand, EU-loaded nano-emulsions (900 µm)-treated E. coli showed a clear peak shift for a membrane protein, lipids, DNA and carbohydrates. This study provides insights to utilize plant phenols as safe medicines as well as dietary supplements.