Lactobacillus rhamnosus GG (LGG) and Lactobacillus acidophilus NCFM (LNCFM) were encapsulated in alginate microgel particles (microbeads) by a novel dual aerosols method. The encapsulated probiotics in microbead gel matrix were further stabilized in maltodextrin solids by either spray or freeze-drying to form probiotic microcapsule powders. The free cells of probiotics were also sprayed and freeze-dried in maltodextrin only without microgel encapsulation. After rehydration of microgel-encapsulated powder, gel particles regained their shape. There was no difference in the loss of viability between encapsulated and unencapsulated probiotics during spray drying or freeze-drying. For LNCFM, spray-dried bacteria with or without gel encapsulation exhibited less death (3.03 and 3.07 log CFU/g reduction, respectively) than those of freeze-dried bacteria (4.36 and 4.89 log CFU/g reduction, respectively) after 6 months storage at 4 °C. The same trend was also observed in spray-dried LGG without gel encapsulation which showed 5.87 log CFU/g reduction in viability after 6 months at 4 °C; however, freeze-dried LGG without gel encapsulation exhibited a rapid reduction in viability of 5.91 log CFU/g within just 2 months. Gel-encapsulated LGG which was freeze-dried exhibited less death (3.32 log CFU/g reduction) after 6 months at 4 °C. This work shows that spray drying results in improved subsequent probiotic survivability compared to freeze-drying and that alginate gel encapsulation can improve the survivability following freeze-drying in a probiotic-dependent manner.