White soft cheese is extremely vulnerable to contamination from a range of pathogenic and/or spoiling microorganisms during handling, production, and storage. Therefore, this study was aimed to investigating the characterization of NEs of Thyme and Clove EOs, as well as their effects on the sensory and microbiological properties of UF cheese along the storage period of 50 days at 7 °C. Therefore, the nanoemulsions (NEs) of thyme and clove essential oil (EO) were prepared by ultrasonication (as delivery systems) to be utilized as a natural preservative for ultrafiltered (UF) soft cheese. The prepared NEs were characterized by dynamic light scattering (DLS) for particle size. Different concentrations of Thyme NE (0.03, 0.06, and 0.1%) as well as Clove NE (0.06, 0.1, and 0.25%) were used to preserve UF cheese. The microbiological analysis and sensory evaluation of different UF cheese treatments were evaluated during a cold storage period of 50 days. The results revealed that the droplet size of the prepared NEs was 94.85 and 68.67 nm for Thyme and Clove NE, respectively. According to the sensory analysis, soft cheese fortified with NEs was still acceptable. The highest sensory acceptance was related to the cheeses fortified with 0.03% and 0.06% Thyme and Clove NE, respectively. The results of microbial groups indicated that NEs of both EOs added to retentate led to a decrease in the total bacterial count (TBC), compared with the control. The growth of psychrotrophic bacteria, as well as yeast and mold, was inhibited by the concentrations of 0.1% and 0.25% of thyme and clove NE, respectively, until the end of the storage period. These findings recommend using NEs of thyme and clove oils as natural preservatives to maintain the quality of soft cheese and prolong its shelf life.