Final sterilisation of drug-loaded polymeric microspheres is problematic as dry heat or steam sterilisation are not applicable, and γ-irradiation may result in radiolytic scission of the polymer chains, and potentially damage the bioactive compound. Therefore, aseptic production is the method of choice to obtain a sterile product. A novel process for the production of microspheres is introduced based on the principle of double emulsion–solvent extraction. The process uses a flow-through ultrasonic cell for the preparation of the primary emulsion, in combination with a static micromixer for the production of the double emulsion. Because of its small scale, the equipment is readily accommodated in a laminar air-flow cabinet or an isolator. Thanks to the low technical complexity and easy handling of the process, only minimal manual interventions is required. Finally, the possibility for in-place cleaning and sterilisation makes the equipment and process well suited for aseptic microsphere preparation. Microspheres were prepared from poly(lactic-co-glycolic acid) (PLGA), and bovine serum albumin (BSA) served as model protein for microencapsulation. The BSA-in-PLGA (w/o) emulsions produced by the ultrasonic flow-through cell exhibited mean droplet sizes of <700 nm. Further processing into microspheres of 15–40 μm mean diameter resulted in approx. 70% BSA encapsulation efficiency. Batch-to-batch reproducibility was excellent. Microsphere batches produced under aseptic conditions to assure product sterility exhibited no microbial contamination when examined by a simplified sterility test. The presented technology offers great potential for aseptic microsphere production for batch-sizes suitable, e.g. for clinical investigations. Complete validation of product sterility would, however, demand more extended tests.