Nanotechnology applications have been employed to improve the stability of bioactive components and drug delivery. Natural-based extracts, especially olive leaf extracts, have been associated with the green economy not only as recycled agri-waste but also in the prevention and treatment of various non-communicable diseases (NCDs). The aim of this work was to provide a comparison between the characteristics, biological activity, and gene expression of water extract of olive leaves (OLE), green synthesized OLE silver nanoparticles (OL/Ag-NPs), and OLE whey protein capsules (OL/WPNs) of the two olive varieties, Tofahy and Shemlali. The particles were characterized by dynamic light scattering, scanning electron microscope (SEM), and Fourier transform infrared. The bioactive compounds of the preparations were evaluated for their antioxidant activity and anticancer effect on HCT-116 colorectal cells as well as for their regulatory effects on cytochrome C oxidase (Cox1) and tumor necrosis factor α (TNF-α) genes. (OL/Ag-NPs) were found to be smaller than (OL/WPNs) with sizes of (37.46±1.85 and 44.86±1.62 nm) and (227.20±2.43 and 553.02±3.60 nm) for Tofahy and Shemlali, respectively. SEM showed that Shemlali (OL/Ag-NPs) had the least aggregation due to their highest Ƹ-potential (-31.76 ± 0.87 mV). The preparations were relatively nontoxic to Vero cells (IC50 = 151.94–789.25 μg/mL), while they were cytotoxic to HCT-116 colorectal cells (IC50 = 77.54–320.64 μg/mL). Shemlali and Tofahy OLE and Tofahy OL/Ag-NPs had a higher selectivity index (2.97–7.08 μg/mL) than doxorubicin (2.36 μg/mL), indicating promising anticancer activity. Moreover, Shemlali preparations regulated the expression of Cox1 (up-regulation) and TNF-α (down-regulation) on HCT-116 cells, revealing their efficiency in suppressing the expression of genes that promote cancer cell proliferation. (OL/Ag-NPs) from Tofahy and Shemlali were found to be more stable, effective, and safe than (OL/WPNs). Consequently, OL/Ag-NPs, especially Tofahy, are the best and safest nanoscale particles that can be safely used in food and pharmaceutical applications.