The effect of encapsulation on the survival of Lactobacillus plantarum during isothermal heating and bread baking was investigated. Four encapsulating materials were evaluated, i.e., reconstituted skim milk (RSM), gum arabic (GA), maltodextrin (MD) and inulin. Freeze dried bacteria survived better in GA and RSM matrices during isothermal heating at 90 °C, which was explained by their high glass transition temperatures and physical entrapment of the bacterial cells in their dense microstructure. The survival of bacteria in bread during baking depended on the approach used to incorporate probiotics and physical properties of encapsulating materials, which was related to the exposure of the bacterial cells to moist-heat. Maximum survival of probiotic bacteria (>108 CFU/g bread) was achieved after 15 min baking at 100 °C when the RSM-probiotic powder was distributed on the dough surface. Furthermore, A Weibull model could describe the general trend of the inactivation kinetics of bacteria during isothermal heating (at 60, 75 and 90 °C) as influenced by the initial moisture content of the RSM-water mixtures (0.05, 0.60 and 0.90 kg/kg). Future development of bakery products with alive probiotic bacteria could benefit from this work.