The objective of this work was to design a new drug nanoparticle (NP) composed of chitosan/β-cyclodextrin/sodium tripolyphosphate/alginate (CS/βCD/TPP/AL) loaded with a clove extract (CE) for potential anticancer effects. The extract was prepared by two extraction methods: hydroalcoholic maceration (MAC) with 80% MeOH and supercritical fluid (SCF). The MACCE and SCFCE CE NPs had particle sizes of 71 nm and 20 nm, respectively with irregular spherical shapes. The nanocarriers achieved entrapment efficiencies of over 90%. MACCE-NPs and SCFCE-NPs released 18.35% and 10.12% of the extract after 6 h, respectively. Cell viability decreased to 54%, 7%, and 12% in HeLa, U87, and KB cell lines, respectively, after a 48-hour treatment with SCFCE-NPs and 75%, 8%, and 17% after treatment with MACCE-NPs, significantly reduced compared to the control. It is concluded that NPs containing CE exhibit a higher degree of toxicity due to better penetration into cells.