The extraction of soluble hydrolysate protein and sugar from a biomass cocktail of defatted soybean meal (DSM) and jackfruit peel (JP) was examined using microwave-alkaline hydrolysis by varying the NaOH concentrations (0.04-0.11 M) and residence times (2-11 min). Based on the central composite design, the optimized parameters were achieved at 0.084 M NaOH concentration (100 mL), for 8.7 min at 300 W microwave power level to obtain the highest protein (5.31 mg/mL) and sugar concentrations (8.07 mg/mL) with > 75% recovery. Both raw and detoxified hydrolysate (using activated carbon) were correspondingly biocompatible with Enterobacter hormaechei strain 40a (P > 0.05) resulting in maximal cell counts of > 10 log CFU/mL. The optimized hydrolysate was prepared as an additive in molasses-alginate bead encapsulation of strain 40a. Further evaluation on phosphate and potassium solubilization performance of the encapsulated strain 40a exhibited comparable results with those of free cell counterpart (P > 0.05). The DSM-JP hydrolysate cocktail holds potential as a carrier additive of encapsulated-cell bead biofertilizers in order to sustain bacterial cell quality and consequently improve crop growth and productivity.