In this study, the main goal was to identify an effective alternative method to protect Ready-to-Eat (RTE) food from foodborne pathogens. Thyme (Thymus vulgaris L.) and rosemary (Rosmarinus officinalis L.), originating from Mediterranean countries, particularly Egypt, contain numerous bioactive phytochemicals, notably polyphenols and flavonoids. These herbs are commonly utilized as flavor enhancers, spices, and preservatives. The ethanolic extracts (70 %) of rosemary and thyme (EER and EET) were analyzed using gas chromatography-mass spectrometry (GC–MS) and high-performance liquid chromatography (HPLC). The antioxidant and antimicrobial activities of EER and EET were assessed for their ability to reduce the growth of pathogenic bacteria, including Gram-positive i.e. Listeria monocytogenes Scott A and Staphylococcus aureus ATCC 6538, and Gram-negative i.e. Escherichia coli ATCC 8739 and Salmonella enterica PT4, both in vitro and in refrigerated cottage cheese over 50 days. Variations in the physicochemical and sensory characteristics of cheese through storage were also monitored. Pasteurized milk (72 °C for 15 s) was renneted after being injected with a mixed culture of L. monocytogenes and S. enterica at a concentration of roughly 3.0 log CFU/mL. In situ supplementation with EER and EET demonstrated antimicrobial effects against these pathogens in cottage cheese samples. Supplementation of cottage cheese with EER and/or EET (0.5 or 1.0 %, w/w) significantly reduced pathogen counts by approximately 2.0 log CFU/g after 30 days of storage. EER and EET also inhibited the development of titratable acidity, decreased alterations in ripening indicators and flavor components, and maintained the cottage cheese's physicochemical and sensory qualities throughout the storage duration.