A randomized case control prospective method was adopted in this study in order to assess the health benefit associated with the Darfiyeh cheese, a traditional Lebanese raw goat milk cheese ripened in goat skin. 21 participants were recruited and divided into 2 groups: test group (n = 10) and control group (n = 11). Venous blood and stools were collected at day 14, 21 and day 0 and 21 respectively. Flow cytometry was performed on blood sample. Fecal samples were plated on Plate Count Agar (PCA) and de Man, Rogosa and Sharpe Agar (MRS) agar in order to monitor any alteration in the gastrointestinal tract (GIT). At day 24, a significant increase by 27.67% (p = 0.043) in the bacterial count was seen on the MRS agar for the test group in comparison to no change in the total bacterial count. At day 14 a significant drop (p = 0.026) in CD3+/CD4+ population in the test group (35.67 vs 42.87), and a non-significant drop (p = 0.818) in CD8+ (24.76 vs 28.28) is seen when compared to control group. At day 24, no significant change (p = 0.20) in the CD3+/CD4+ population in comparison between both groups and no change in CD8+ or Geo means in both groups. In conclusion, an alteration in the GIT microflora could be hinted at by the lactobacilli bacterium, which was not reflected on the total bacterial count.