The development of microalgae-based agricultural biostimulants requires integrated production strategies that ensure biomass availability, formulation stability, and process scalability. This study developed and evaluated a pilot-scale production system integrating Scenedesmus sp. cultivation in a raceway reactor with the formulation and characterization of nanobentonite-stabilized oil-in-water Pickering emulsions. Microalgal biomass production was simulated using a MATLAB-based model and compared with experimental and published raceway data, showing good agreement. Emulsion processing conditions were investigated through experimental designs evaluating agitation speed, mixing time, and draft tube configuration. Among five oils evaluated, corn oil provided the longest microalgal viability half-life (145 days). A stable Pickering emulsion was obtained using 4 wt% nanobentonite and a 50:50 oil-to-water ratio. Fluorescence microscopy revealed microalgal cells dispersed in the aqueous phase and associated with oil droplets. Operating conditions of 2000 rpm and 10 min were selected for scale-up, while statistical analysis identified significant effects of mixing time, draft tube configuration, and their interaction on emulsion stability at extended processing times. Rheological characterization revealed yield-stress and shear-thinning behavior, adequately described by the Herschel–Bulkley model, indicating structural stability at rest and favorable flow properties during processing. Furthermore, the emulsion enhanced biostimulant performance compared with microalgae applied at an equivalent dose in water, increasing the germination index by approximately 200% relative to the positive control. Overall, these findings highlight the potential of integrating microalgal cultivation, formulation development, and process optimization to produce stable and effective agricultural biostimulants with potential for scale-up.