Milk rice pudding (MRP) is a commercial and popular dairy dessert, but owing to its characteristics and valuable ingredients, it may be contaminated by many pathogenic and spoilage microorganisms. So, this study aimed to improve the quality and safety of MRP by using cinnamon and clove essential oils. Concerning the evaluation of the minimum inhibitory concentration (MIC) for both oils with 0.2, 0.5, and 1% concentrations, B. cereus and B. subtilis were sensitive (+) to cinnamon and clove 0.5%, with inhibition zones of 13.3 and 14 mm for cinnamon and 11.3 and 12 mm for clove EO, respectively. While both bacteria were very sensitive (++) to cinnamon 1% (18.8 and 19.5 mm) and clove 1% (17.3 and 18.7 mm), respectively. Therefore, MRP was prepared by adding cinnamon and clove EOs at 0.6%. Treatments containing EOs showed a significant reduction of tested microorganisms compared to controls. B. cereus wasn’t detected in clove and cinnamon EO treatments at day 21 of the storage period, while B. subtilis vanished on day 14 for the cinnamon treatment and on day 21 for clove MRP. Moreover, the results revealed the enhancement of sensory characteristics of MRP supplemented with EOs without any significant alteration in their pH values. This study recommends the addition of cinnamon and clove EOs (0.6%) to MRP, as it isn’t only an excellent substitution of chemical preservatives with powerful antibacterial efficiency but also improves the overall acceptance of the product.