Strong antileishmanial and antitrypanosomal activities were highlighted for the crude methanolic extract (IC50 = 0.61 and 2.15 mu g/mL, respectively) of Zanthoxylum zanthoxyloides (Lam.) B.Zepernick & Timler root bark, as well as for its apolar partitions (cyclohexane: IC50 = 0.66 and 5.17 mu g/mL, respectively and dichloromethane: IC50 = 0.07 and 0.22 mu g/mL, respectively), with a good selectivity index (SI) towards WI-38 cells. In addition, cyclohexane and dichloromethane extracts exhibited a dose-dependent inhibition of human coronavirus HCoV-229E infection in hepatoma Huh-7 cells expressing or not the cellular protease TMPRSS2 (IC50 values of 5.29 mu g/mL and 4.87 mu g/mL, respectively). Fractionation of these active extracts led to the isolation of a new racemic benzophenanthridine alkaloid named zanthoxyloithrine (1), together with 13 known compounds. Their structures were elucidated by spectroscopic techniques including IR, UV, HR-MS, 1D and 2D NMR and electronic circular dichroism. In parallel, HR-ESI-MS/MS based dereplication and molecular networking analysis were performed to identify unpurified compounds in cyclohexane and dichloromethane extracts. Zanthoxyloithrine (1) showed strong antileishmanial (IC50 = 0.14 mu M, SI = 52.0) and antitrypanosomal (IC50 = 0.36 mu M, SI = 20.8) activities. In addition, compound (1) demonstrated a high antiviral activity against HCoV-229E with IC50 value of 6.70 mu M in presence of TMPRRS2 and without significant toxicity on Huh-7 cells. Other purified benzo[c]phenanthridine alkaloids also showed anti-coronavirus and antiparasitic activities.