This study evaluated the effect of two inactivation methods on probiotic, and aimed to determine a suitable inactivation method and condition for obtaining beneficial paraprobiotics from Lactobacillus plantarum (LP) and Lactobacillus gasseri (LG). The effect of inactivation condition on culturability, physiological properties, and morphological characteristics was evaluated by a plating method, flow cytometry, and field emission-scanning electron microscopy, respectively. The result revealed that each strain conferred different resistance to inactivation methods. The heat-treated (75 and 90 °C for 15 and 30 min) LG lost its growth ability, but it's all sonicated samples (50 and 100 W for 5 and 10 min) were stable and maintained their growth ability. However, the ability to grow on culture media of sonicated (50 and 100 W for 5 and 10 min) LP was less than its heat-treated (75 and 90 °C for 15 min) specimens. According to flow cytometry data, the membrane integrity of each probiotic cell was affected by both inactivation methods; however, the severe heat process (90 for 30 min) causes the most serious membrane damage to LG cells (PI = 97.7%). Morphological properties of both strains were significantly affected by inactivation methods. After inactivation treatment, damaged cell, cell roughness, lysed cell, cell adhesions, cell disruption, and cell bending were increased, significantly. Results indicate that for obtaining a functional paraprobiotic the inactivation process should be optimized. Also, it should be noticed that a particular optimized inactivation method is not suitable for obtaining paraprobiotic from all probiotic strains.