Two strains of γ-aminobutyric acid (GABA) producing bacteria, L. brevis Y1 and L. plantarum LM2, were microencapsulated in sodium alginate with two concentrations (1% and 2%) of monosodium glutamate (MSG) by using vibrating technology. The mix of both species was microencapsulated both in fresh and freeze-dried form. After 0, 1, 2, and 4 weeks of storage at 4 °C in quarter strength Ringer’s solution, the microcapsules were subjected to cell viable counting and sub-cultured in MRS at 37° for 24 h. The MRS cultures were analyzed for the GABA content. The amount of GABA produced per CFU of MRS inoculum was then calculated. Only the 4-week-old microcapsules were used to inoculate a chocolate milk drink with the aim of obtaining a functionalized drink containing viable probiotic cells and GABA after a 1-week incubation at 4 °C. Therefore, the GABA production in chocolate milk per CFU of the probiotic culture after the incubation time was calculated. Results of the GABA analysis by liquid chromatography mass spectrometry of the MRS sub-cultures showed no significant difference (p > 0.05) in GABA yield between 1% and 2% MSG for the microcapsules containing fresh cells. On the contrary, a significant difference (p < 0.05) in productivity along the storage was registered. Microcapsules containing freeze-dried cells showed significant differences (p < 0.05) in GABA yield between 1% and 2% MSG only after 2 and 4 weeks of storage. A significant difference (p < 0.05) in GABA yield between the storage time was found only for the trials with 2% MSG for freeze-dried cells. The synthesis of GABA in chocolate milk significantly decreased (p < 0.05) only for fresh cells when comparing 2% with 1% MSG. In conclusion, a 1-month storage of microcapsules containing both culture forms, fresh and freeze-dried, did not affect GABA production.