Multi-strain aerobic/anaerobic probiotic mixtures have gained considerable attention recently in terms of both food supplementation and therapeutic applications. The efficiency of such probiotic mixtures depends on the viable cell count in the gastrointestinal tract. Conventionally, probiotics are produced in individual bioreactors and supplemented with specific prebiotics and carrier agents to enhance performance. However, the production of multi-strain probiotic products is expensive. Hence, novel probiotic production strategies are crucial. This review describes conventional methods of probiotic production, followed by a comparative discussion of various alternative fermentation methods. We describe strategies to enhance the shelf-life of probiotic strains and the role of immobilization and carrier molecules in the production and harvesting of multi-strain aerobic/anaerobic probiotics. Finally, we discuss the role of novel materials and strategies that could potentially reduce the production cost associated with probiotics. Such novel strategies could potentially produce and encapsulate multiple probiotic strains in a single step.