Plants traditionally used for their antiviral activity could be an alternative against SARS-CoV-2. In this study, the efficacy of 10 bioactive plant compounds commonly used in Mexico against COVID-19 was evaluated by molecular docking with two online servers: COVID-19 Docking Server and DockThor. Remdesivir was used as a control. The results showed that Cypellocarpin B, Cypellocarpin C, Luteolin 7-glucoside and Syringetin glucopyranoside showed the highest affinity towards viral proteins Mpro and RdRp respect to Remdesivir. Comparison of molecular docking servers showed differences in the docking motors and proteins available on each server. The use of bioactive compounds represents an alternative for the treatment of patients with COVID-19.