Essential oils (EOs), such as thyme essential oil (TEO), are widely known for their antimicrobial properties; however, their direct application in food systems is limited due to their poor stability, which affects their efficacy. This study aims to improve the stability and antimicrobial efficacy of TEO by encapsulating it in Pickering emulsions stabilized with cellulose nanocrystals (CNC). Two formulations of Pickering emulsions with 5% and 10% TEO were prepared and compared to traditional surfactant-based emulsions. The stability of the emulsions was assessed over 21 days, and particle size, zeta potential, Raman spectroscopy, and FTIR were used for characterization. The antimicrobial activity was tested against several foodborne pathogens, with minimum inhibitory concentration (MIC) values determined. The 10% TEO Pickering emulsion showed antimicrobial activity, with MIC50 values of 4096 µg/mL against Staphylococcus aureus and Escherichia coli, while the 5% TEO formulation had no effect at MIC50 > 8192 µg/mL. The CNC-stabilized Pickering emulsions exhibited superior stability, showing no phase separation over 21 days. The findings suggest that CNC-stabilized Pickering emulsions are effective at improving the stability and antimicrobial performance of TEO, making them a promising natural preservative for food packaging and safety. Further research is recommended to optimize the formulation and broaden TEO’s application in food preservation.