Tallaga cheese is the most popular type of white soft cheese in Egypt. Cronobacter sakazakii is an opportunistic foodborne pathogen that poses a threat to the health of almost every age group, with a particular emphasis on neonates and infants. Essential oils (EOs), such as olive oil and thyme oil, exhibit a broad-spectrum antibacterial effect. However, few studies have investigated the antibacterial activity of these EOs and their formulated nanoemulsions (NEs)—olive oil nano-emulsions (ONE) and thyme oil nano-emulsions (TNE)—on C. sakazakii in cheese to date. The purpose of this study was to investigate the inhibitory effects of these EOs and their NEs on the development of C. sakazakii during the processing and storage of Tallaga cheese. Additionally, the organoleptic properties of the resulting cheese were evaluated. Herein, ONE and TNE were prepared and characterized using a zetasizer and transmission electron microscopy (TEM). Furthermore, the minimum inhibitory concentrations (MICs) of EOs and NEs were determined using well diffusion assay. Fresh buffalo's milk for the elaboration of Tallaga cheese was inoculated with C. sakazakii at a concentration of 6 log CFU/mL, along with the addition of MICs of either EOs or NEs. The obtained results showed that the MICs were 15 mg/mL (v/v) for either olive oil, thyme oil, ONE and TNE with diameter inhibition zones of 10.3 ± 0.5, 13.3 ± 1.7, 12.3 ± 0.5, and 16 ± 0.8 mm, respectively. In addition, NEs exhibited high antibacterial activities against C. sakazakii in comparison to pure EOs. Particularly, the strongest antibacterial effect toward C. sakazakii was reported with TNE during manufacturing and storage of Tallaga cheese. Overall, these results suggest that thyme and its NEs have the potential to prevent bacterial contamination by C. sakazakii in the dairy industry.