Background: Viral infections pose a great burden for humankind and many viruses have no effective treatments. Hepatitis A Virus (HAV) and Coxsackie-B4 (Cox- B4) are common viruses having many drawbacks. Using plant extracts as antiviral agents is a globally applied approach due to its efficacy and minimal adverse effects. Objective: This study aimed to test the antiviral action of the green coffee extract against HAV and Cox-B4 viruses, assess the possible mechanisms regulating this role, and apply molecular docking to evaluate the connection between bioactive compounds in the green coffee extract and viral proteins and receptors. Methods: The antiviral effect of four plant extracts, including green tea, green coffee, pomegranate peel, and orange peel on HAV and Cox-B4 viruses has been screened in this study. The most promising results have been obtained using an inverted microscope and electron microscopy. Gas Chromatography-Mass Spectrometry (GC-MS) has been used to detect various compounds in the green coffee extract. Gene expression of MxA has been examined in different groups of treatments. Oxidative enzymes, including Glutathione (GSH), Superoxide Dismutase (SOD), and Malondialdehyde (MDA) were tested in infected Vero cells (African green monkey kidney cells) and upon using green coffee. In silico studies were performed using molecular docking software. Results: Green coffee has been found to have an antiviral impact on HAV and Cox-B4 with IC50= 8.8±0.6 and 14.5±0.8 μg/ml, respectively, visualizing and confirming the results using both Transmission Electron Microscope (TEM) and inverted microscope. The green coffee extract has been found to regulate oxidative enzymes, including SOD, GSH, and MDA, to normal concentrations as well as MxA gene expression to regular levels. Linoleic acid and arachidic acid have been found to be the most common molecules in green coffee extract, interacting with the tested viruses. Conclusion: Green coffee methanolic extract has been found to have an efficient antiviral impact on HAV and Cox-B4 viruses, as validated by in vivo investigations.