The development of state-of-the-art moist-heat-resistant microcapsules for a probiotic is described in this report. The survival of the heat-sensitive probiotic Lactobacillus acidophilus upon exposure to moist-heat treatment was improved by encapsulating the bacterial cells in multilayered microcapsules, which were formed via a technique that combined electrospraying and fluidized bed coating. A composite composed of egg albumen (EA) and stearic acid (SA) was coated onto the L. acidophilus-encapsulating alginate microcapsules to produce the first shell layer. These microcapsules were subsequently coated with cassava starch granules while they were dried in a fluidized bed dryer using cassava pearls as the drying aid. The effect of the EA:SA ratio on the morphology, encapsulation efficiency (EE) and degree of moist-heat resistance (at 70 °C and 100% relative humidity for 30 min) of the microcapsules was investigated. The results showed that the EE of the microcapsules was greater than 90%. When the relative proportion of SA was increased, the survival rate of the cells encapsulated in the moist-heat-treated microcapsules significantly improved. Compared with earlier reports, the current multilayered microcapsules conferred an extremely high degree of protection of the encapsulated cells upon moist-heat exposure, with the cells suffering a loss of vitality of only 0.6 log CFU/g. These newly developed microcapsules can serve as a prototype encapsulation structure for the protection of other thermosensitive microorganisms and compounds used to fortify foods and feeds.