Lensoside Aβ (LAβ) is a quercetin derivative isolated from the leaves and stems of the Lens culinaris cultivar Tina. Flavonoid-membrane interactions are crucial for their physiological and pharmacological activity. We have demonstrated the impact of LAβ on EYPC liposomes resembling the lipid phase of tumor cell membranes with the use of the 1H NMR technique and have examined its activity on HeLa cells for the first time. To study the interactions of the tested compound with lipids and proteins at the molecular level, the FTIR technique was applied. To reveal changes in morphology and ultrastructure as well as examine its effect on apoptosis induction and cell viability, SEM, TEM, light, and fluorescence microscopy, flow cytometry analysis, LIVE/DEAD assays were employed. The ability of LAβ to induce oxidative stress was determined by staining with DHR123. The FTIR analyses indicated that LAβ interacts with the PO2− groups in the polar head region. Moreover, a decrease in the relative protein concentration and changes in protein spectral profile in the amide I region were noted. Flavonoid reduced the viability of HeLa cells, which was correlated with the induction of apoptosis supported by SEM and TEM observations. Moreover, the addition of lensoside Aβ induced oxidative stress. These results confirm that lensoside Aβ may be used in novel therapeutic approaches for treating cervical cancer.