Summary Over the past few decades, considerable interest has been shown in developing nano‐ and microcarriers with biocompatible and biodegradable materials for medical and biotechnological applications. Microencapsulation is a technology capable of enhancing the survival rate of bacteria, providing stability in harsh environments. In the present paper, we developed a technology to encapsulate microorganisms within polyhydroxyalkanoate ( PHA )‐based microcapsules ( MP s), employing a modified double emulsion solvent evaporation technique, with Pseudomonas putida KT 2440 as a biotechnological model strain. The resulting MP s display a spherical morphology and an average particle size of 10 μm. The stability of the MP s was monitored under different conditions of storage and stress. The MP s remained stable for at least 24 days stored at 4°C in a water suspension. They exhibited greater tolerance to stress conditions; encapsulated cells remained viable for 2 h in alkaline solution and after 24 h of H 2 O 2 exposure at 10 and 20 mM. Results suggested the potential of MP s as a microcontainer of bacterial cells, even for biotechnological applications requiring high alkaline conditions and oxidative stress. We validated the potential applicability of the PHA ‐based microencapsulation method in other microorganisms by encapsulating the predatory bacterium Bdellovibrio bacteriovorus .