This study aims to estimate the in situ effect of Phoenician juniper leaves on the physicochemical and microbiological quality of fermented goat's milk stored under ambient conditions. In this study, we used two samples. The first sample was goat's milk flavored with juniper leaves, compared to the control sample without juniper leaves. We analyzed three physicochemical parameters: pH, titratable acidity, and temperature. Furthermore, the bacteriological analysis focused on the following parameters: Total aerobic mesophilic flora (TAMF), total coliforms (TC), fecal coliforms (FC), coagulase-positive Staphylococci (CoPS), and pathogenic bacteria (Salmonella spp and Listeria monocytogenes). The physicochemical results showed a change in the pH and titratable acidity of both samples with a higher acidity for the test sample compared to the control sample. This change was marked by an increase in a load of total aerobic mesophilic flora and lactic acid bacteria, a decrease in the total coliforms and thermotolerant coliforms, and the Staphylococci load in the test sample compared to the control sample, which experienced an increase in these bacterial parameters. For the test sample, juniper leaves reduced bacterial contaminants in fermented goat's milk by 38% for total coliforms, 41% for fecal coliforms, and 89% for staphylococci. Both samples were free of Salmonella spp and L. monocytogenes. These results are probably due to the effect of bioactive compounds of Juniperus phoenicea L leaves known for their antimicrobial effect. This traditional practice of our ancestors can improve the quality of fermented goat's milk stored even at ambient temperature.