Microencapsulation of lactic acid bacteria (LAB) via spray drying differs from that of common bioactive substances in that the intrinsic stress tolerance of cells can be modulated to improve cell survival. In this study, elevated growth temperatures that were 3–5 °C above the standard conditions were used to culture Lactococcus lactis subsp. cremoris , Lactobacillus rhamnosus GG (LGG), and Lactobacillus acidophilus for spray drying. The heat-adapted cultures showed lower bacterial population than the controls by 0.45 log at stationary growth phase and produced lactobacilli cells with elongated shape, while their metabolic activities were maintained similar to the controls. Heat-adapted L . cremoris and LGG demonstrated increases in survival by 0.7–1.5 log and 0.3 log, respectively, after heat treatment at 60 °C. The thermotolerance of L . acidophilus grown at 42 °C was dependent on growth phase, and the culture entered death phase within 24 h of incubation. The survival of heat-adapted L . cremoris and L . acidophilus after spray drying was increased by 21.0% and 13.7%, respectively, whereas the increase shown by LGG was relatively insignificant (9.9%). Spray-dried powders containing heat-adapted cells showed substantial reduction of viability at the first week of storage, reaching 1.03–1.23 log, compared to 0.87–0.90 log of reduction shown by the controls. The findings demonstrated that strain-specific cellular response toward variations in growth conditions is crucial to the intrinsic properties of LAB and to cell survival during spray drying and storage. Controlling cellular response is one of the key factors in developing a viable spray drying scheme for active LAB.