In this study, we present a novel type of microfluidics-based formulation for the delivery of microbial control agents (mBCAs) in soil, where bacterial cells and fungal spores are directly combined into millimeter-sized alginate capsules. This process resulted in the reproducible production of 500 μm sized beads in a good throughput for this type of biofluid (up to 48 beads/min). A subsequent chitosan coating (1-2 μm-thick) provided a good storage stability at 3 months, with 100% microcapsules containing viable fungal biomass and 60-80% with viable bacterial cells depending on the species. This novel formulation was tested both in the greenhouse and on-farm with lettuces, and encapsulated microbial biomass had a more prominent effect on crop growth and yield, as compared to their delivery as a liquid suspension.