In the present study, nutraceutical citrulline was produced using immobilization of permeabilized whole cells of Pseudomonas furukawaii, an efficient producer of ADI. Since ADI is intracellularly localized, various additives such as SDS, Triton X-100, and EDTA were used to permeabilize the cell to improve substrate accessibility and ADI activity. The maximum ADI activity was observed with 0.25 mg mL−1 biomass concentration treated with 0.5 mmol L−1 EDTA for 15 min using OFAT approach. Optimization of permeabilization conditions of P. furukawaii cells using novel neural networks and particle swarm optimization (PSO-NN) led to maximum ADI activity with 0.10 mmol L−1 EDTA and 0.30 mg mL−1 biomass. Further, the morphological characterization of immobilized cells was assessed by FESEM and FTIR. An optimal citrulline production of 1.19 mmol L−1 was achieved at 2.5% sodium alginate with 20 mmol L−1 arginine at 38°C, and 180 min of incubation. The immobilized cells retained 90.3% productivity after seven reuse cycles. Thus, the formulated immobilized whole-cell biocatalyst, with higher stability offers cost-effective methods of citrulline production.