The aims of this study were to evaluate the effect of types of protein-based microcapsules and storage at various ambient temperatures on the survival of Lactobacillus acidophilus during exposure to simulated gastrointestinal tract and on the change in thermo-tolerance during heating treatment. The encapsulating materials were prepared using emulsions of protein (sodium caseinate, soy protein isolate, or pea protein), vegetable oil, and glucose, with maltodextrin was used as a wall material. The formulations were heated at 90 °C for 30 min to develop Maillard substances prior to being incorporated with L. acidophilus. The mixtures were then spray dried. The microspheres were stored at 25, 30, and 35 °C for 8 wk and examined every 4 wk. The addition of proteins as encapsulating materials demonstrated a significant protective effect (P < 0.05) as compared to the control sample. Sodium caseinate and soy protein isolate appeared more effective than pea protein in protecting the bacteria after spray drying and during the storage at different room temperatures. Storage at 35 °C resulted in a significant decrease in survival at end of storage period regardless the type of encapsulating materials. The addition of protein-based materials also enhanced the survival of L. acidophilus during exposure to simulated gastrointestinal condition as compared to the control. After spray drying and after 0th wk storage, casein, soy protein isolate, and pea protein-based formulations protected the bacteria during heat treatment. In fact, a significant decrease in thermal tolerance was inevitable after 2 wk of storage at 25 °C.