Isophane insulin (N) is challenging to administer orally due to its gastrointestinal instability. Research has shown that partially complexing N with hydroxypropyl β-cyclodextrin (HPβCD-N complexes) enhances its stability. Nanoparticles (NPs) are also frequently used to encapsulate drugs to protect them from degradation. This study aimed to optimize HPβCD-N complex-loaded thiolated chitosan/alginate (TCS/ALG) NPs using a full factorial design. The HPβCD-N complexes were prepared before being loaded into the NPs. Independent variables included the concentrations of TCS, ALG, and HPβCD-N complex, while the dependent variables were particle size and zeta potential. The results demonstrated that TCS and ALG concentrations had a positive and negative effect on particle size, respectively, with smaller particles being favored. The zeta potentials of the NPs increased positively and negatively in proportion to the TCS and ALG concentrations, respectively. The HPβCD-N complexes had a minimal effect on the dependent variables. The NPs made with TCS, ALG, and HPβCD-N complex concentrations of 0.075%, 0.0375%, and 5% w/w, respectively, were the most suitable for achieving small particle size and zeta potential within +30 mV and +50 mV. TEM images showed spherical particles with nanometer diameters. The encapsulated N was found to be approximately 1% w/w, confirming successful loading of N into the NPs. Thus, the optimized formulation shows potential as an NP carriers for N delivery.