Sodium alginate (SA) at 2% (w/v) and low acylated gellan gum (LAG) at 0.2% (w/v) were used to microencapsulate Lactobacillus helveticus and Lactobacillus delbrueckii spp lactis by employing the internal ionic gelation technique through water–oil emulsions at three different stirring rates: 480, 800 and 1200rpm. The flow behavior of the biopolymer dispersions, the activation energy of the emulsion, the microencapsulation efficiency, the size distribution, the microcapsules morphology and the effect of the stirring rate on the culture viability were analyzed. All of the dispersions exhibited a non-Newtonian shear-thinning flow behavior because the apparent viscosity decreased in value when the shear rate was increased. The activation energy was calculated using the Arrhenius-like equation; the value obtained for the emulsion was 32.59kJ/mol. It was observed that at 400rpm, the microencapsulation efficiency was 92.83%, whereas at 800 and 1200rpm, the stirring rates reduced the efficiency to 15.83% and 4.56%, respectively, evidencing the sensitivity of the microorganisms to the shear rate (13.36 and 20.05s−1). Both optical and scanning electron microscopy (SEM) showed spherical microcapsules with irregular topography due to the presence of holes on its surface. The obtained size distribution range was modified when the stirring rate was increased. At 400rpm, bimodal behavior was observed in the range of 20–420μm; at 800 and 1200rpm, the behavior became unimodal and the range was from 20 to 200μm and 20 to 160μm, respectively.