<p>Chitosan nanoparticles are widely explored for oral drug delivery. Eudragit S 100 polymer coating changes the modality and drug release behaviour of Chitosan nanoparticles upon oral administration. This study aimed to develop, optimise and understand the drug release mechanism from Eudragit-S100 coated β-cyclodextrin-Chitosan nanoparticle aiming improved oral delivery of indomethacin to colonic region for its possible applications in ulcerative colitis. First, in silico host-guest interaction was used to evaluate the binding affinity of drug with the α, β, and γ-cyclodextrins. Later, the selected indomethacin-β-cyclodextrin inclusion complex was subsequently encapsulated into the Chitosan nanoparticles using the ionic gelation method, followed by Eudragit S 100 coating by dropwise addition of an acetone solution of Eudragit S 100 to the Chitosan nanoparticles dispersion under stirring. The process of Chitosan nanoparticles development was screened and optimized using Quality by Design approach i.e., Taguchi design, and Central Composite Design. The selected independent parameters were pH of the chitosan solution and sonication time, while the responses were encapsulation efficiency (EE%), particle size, and zeta potential, characterized using DLS (Size/PDI/Zeta), TEM morphology, FTIR, stability testing and in vitro release under simulated GI conditions. The optimised nanoparticles had a mean size of 275.66 ± 15.59&#xa0;nm, a zeta potential of + 27.3 ± 1.06 mV, and a high EE% of 86.42 ± 1.77%. TEM confirmed spherical morphology of nanoparticles. Eudragit S 100 coating resulted in charge reversal leading to pH-responsive protection. In vitro studies showed that minimal drug release occurred under gastric conditions (&lt; 15%), yet complete sustained release (&gt; 90%) occurred under colonic conditions. This study establishes a novel Eudragit-chitosan-cyclodextrin based nanocarrier system as a strategy for achieving pH-responsive colon-targeted delivery of indomethacin.</p> Graphical Abstract <p></p>