Charged polymersomes are attractive for advanced material applications due to their versatile encapsulation capabilities and charge‐induced functionality. Although desirable, the pH‐sensitivity of charged block copolymers adds complexity to its self‐assembly process, making it challenging to produce charged polymersomes in a reliable manner. In this work, a flow approach to control and strike a delicate balance between solvent composition and pH for self‐assembly is used. This allows for the identification of a phase window to reliably produce of charged polymersomes. The utility of this approach to streamline downstream processes, such as morphological transformation or in‐line purification is further demonstrated. As proof‐of‐concept, it is shown that the processed polymersomes can be used for surface modifications facilitated by charge complexation.