The study was conducted to evaluate the effect of container smoking in combination with the lactoperoxidase (LP) system on microbial quality of milk. Raw cow and goat milk samples were used. The treatments were T1 (control), T2 (activation of the LP system), T3 (container smoking) T4 (container smoking + LP system). All milk samples were examined for titratable acidity (TA), standard plate counts (TBC) and coliform count (CC) after storage at an ambient temperature for 24 h. The TA, CC & TBC in T2 was significantly lower (p < 0.05) than the respective values in T1 at 7 h and 24 h of storage. The TA remained the same as that of the initial level in T2 at 7 h of storage. T2 and T4 showed similar effects on the growth of microorganisms of milk at 7 h and 24 h of storage. TA, CC and TBC in milk samples stored in T3 was significantly lower (p < 0.05) than T1 in both milk at 7 h and 24 h of storage. However, TA, CC and TBC in T3 was significantly (p < 0.05) higher than T4. The strong inhibitory effect of T4 as compared to T3 suggests that container smoking when combined with the LP system exerts synergistic effect on the growth of microorganisms in raw cow's & goat's milk.