To promote the adequate supplementation of probiotics and bioactives in food formulations, this study aimed to develop synbiotic co-microcapsules containing probiotic strain Lactococcus lactis SKL 13 and bioactive compound, namely γ-Aminobutyric acid (GABA), using spray (at the air inlet and outlet temperatures of 110 ± 2 °C and 50 ± 5 °C, respectively, with a feed flow rate of 2.5 mL min−1) and freeze-drying (at - 40 °C temperature, 1 mbar pressure for 12 h) in a ternary exopolysaccharide (such as maltodextrin, dextran, and inulin in a combination of 8.41, 4.59, and 0.40 g/100 mL, respectively) matrix. The freeze-drying resulted in higher probiotic and GABA encapsulation efficiencies of 95.08 and 90.04%, respectively, than spray drying (probiotics: 93.12% and GABA: 83.46%). The absence of diffraction peaks indicated an amorphous metastable state of microcapsules. Only ∼1% reduction in probiotic count and ∼5% decrease in GABA content were observed in dried capsules after 60 days of storage as well as both the powders showed non-significant (p > 0.05) reduction in probiotic count (2.9 and 1.35 log CFU/mL in intestinal and gastric conditions, respectively) and 80% release of GABA after 240 min of simulated gastrointestinal conditions. The Fourier-transform infrared (FTIR) and scanning electron microscopy (SEM) results further confirmed the proper embedding of probiotics and GABA in the dried microcapsules. The lower moisture content (4.15%), good flowability and higher thermal decomposition peaks at an elevated temperature of 308 °C exhibited by spray-dried powder compared to freeze-dried particles indicated their greater potentiality for high-temperature food applications.