Lantana camara L. (L. camara) is a perennial shrub that contains low amounts of alkaloids. In the present study, the magnetic nanoparticles (MNPs) were used to isolate positively charged alkaloids from the methanolic extract of L. camara leaves. The crude alkaloid was fractionated using HPLC to separate the highest peak of the alkaloid fraction (HPAF). The crude alkaloids (CA) and HPAF were tested for their antiproliferative effect against cancer cell lines (MCF-7, HCT-116, and HeLa) and endothelial cells line (EA.hy926) as a standard cell line. Antiangiogenic properties were examined using rat aortic ring assay. HPAF exhibited a profound anticancer effect against MCF-7 and HeLa cell lines (with IC 50 = 0.027 µg / mL and 5.90 µg / mL, respectively, while it displayed reasonably mild cytotoxicity against the HCT-116 cell line (IC 50 = 8.38 µg / mL). The CA also demonstrated a significant anticancer effect against MCF-7 and HeLa and a weak cytotoxic effect against colon cancer HCT-116 cells. Cationic alkaloids displayed selective antiproliferative activity against HeLa while it was utterly safe on the normal test cell line. HPAF demonstrated remarkable antiangiogenic activity in non-toxic doses. Also, cationic alkaloids showed significant antiangiogenic effects. The use of magnetic nanoparticles (MNPs) to separate small quantities of precious compounds is handy and cost-effective.