Quercetin (QRC), a flavonoid found in foods and plants such as red wine, onions, green tea, apples, and berries, possesses remarkable anti-inflammatory and antioxidant properties. These properties make it effective in combating cancer cells, reducing inflammation, protecting against heart disease, and regulating blood sugar levels. To enhance the potential of inclusion complexes (ICs) containing β-cyclodextrin (β-CD) in cancer therapy, they were transformed into nano-inclusion complexes (NICs). In this research, NICs were synthesized using ethanol as a reducing agent in the nanoprecipitation process. By employing FT-IR analysis, it was observed that hydrogen bonds were formed between QRC and β-CD. Moreover, the IC molecules formed NICs through the aggregation facilitated by intermolecular hydrogen bonds. Proton NMR results further confirmed the occurrence of proton shielding and deshielding subsequent to the formation of NICs. The introduction of β-CDs led to the development of a distinctive feather-like structure within the NICs. The particle sizes were consistently measured around 200 nm, and both SAED and XRD patterns indicated the absence of crystalline NICs, providing supporting evidence. Through cytotoxicity and fluorescence-assisted cell-sorting analysis, the synthesized NICs showed no significant damage in the cell line of MCF-7. In comparison to QRC alone, the presence of high concentrations of NICs exhibited a lesser degree of toxicity in normal human lung fibroblast MRC-5 cells. Moreover, the individual and combined administration of both low and high concentrations of NICs effectively suppressed the growth of cancer cells (MDA-MB-231). The solubility improvement resulting from the formation of QRC-NICs with β-CD enhanced the percentage of cell survival for MCF-7 cell types.