This research studied the viability of probiotic bacterium Lactobacillus plantarum (L. plantarum) encapsulated in the internal aqueous phase (W1) of a water‐in‐oil‐in‐water (W1/O/W2) emulsion system, with the help of gelation and different gelling agents. Additionally, the physicochemical, rheological, and microstructural properties of the fabricated emulsion systems were assessed over time under the effect of W1 gelation. The average droplet size and zeta potential of the control system and the systems fabricated using gelatin, alginate, tragacanth gum, and carrageenan were 14.7, 12.0, 5.1, 6.4, and 7.3 μm and − 21.1, −34.1, −46.2, −38.3, and −34.7 mV, respectively. The results showed a significant increase in the physical stability of the system and encapsulation efficiency of L. plantarum after the W1 gelation. The internal phase gelation significantly increased the viability of bacteria against heat and acidic pH, with tragacanth gum being the best gelling agent for increasing the viability of L. plantarum (28.05% and 16.74%, respectively). Apparent viscosity and rheological properties of emulsions were significantly increased after the W1 gelation, particularly in those jellified with alginate. Overall, L. plantarum encapsulation in W1/O/W2 emulsion, followed by the W1 gelation using tragacanth gum as the gelling agent, could increase both stability and viability of this probiotic bacteria.