Recently, due to the chromate and phosphate compounds toxicity and environmental harsh effects, green inhibitors were introduced. Besides, the biocompatible nano-containers were utilized for encapsulating active green inhibitors. In the present research, the β-cyclodextrin, which is a biocompatible/supramolecular type nanocontainer with a high encapsulating capacity of inhibitor, was loaded with the green L-histidine (L-His) amino acid. The inclusion complexes were characterized via different characteristic methods (i.e., XRD, Raman, FT-IR, UV–vis, and TGA), and the particles' morphology was visualized by FE-SEM. The protection performance of the synthesized particles in the solution phase was investigated by EIS/Tafel methods, and the protected substrates were investigated elementally/morphologically via various approaches (i.e., GIXRD, EDS/Mapping, contact angle, and FE-SEM). Evaluation of the β-CD-L-His loaded silane composite coating active inhibition ability was done by the EIS investigations (over the defected composite), and the derived results confirmed the resistance increment from 5540 Ω. cm2 to 12,101 Ω. cm2, approving the desirable active inhibition ability of the designed thin organic-inorganic composite layer. For better evaluation, the defect structure was displayed by FE-SEM and EDS/Mapping microscopies. The excellent durable passive behavior of the inclusion complexes in the intact SiC was depicted by EIS measurements. Besides, the scratched composite coating resistance enhancement (from 13,032 Ω. cm2 to 23,485 Ω. cm2) demonstrated the β-CD-L-His filled SiC coating's excellent active inhibition capacity. Alongside the abovementioned experiments, new fundamental insights concerning the histidine loading capacity, and electronic aspects/adsorption attributes of histidine and histidine/β-CD-based complexes over the target adsorbent were elucidated choosing DFT-D and molecular simulations tools working at electronic/atomic levels.