Melissa officinalis is a perennial medicinal plant traditionally used for its diverse biological activities, including antiviral properties. This study investigates the antiviral efficacy of various extracts, including water, acetone, alkaloid, non-alkaloid, ethanol, and methanol extracts, against influenza A (H1N1), SARS-CoV-2, and MERS-CoV. The water extract demonstrated significant inhibitory effects on SARS-CoV-2 (IC = 421.9 µg/mL) and MERS-CoV (IC = 222.1 µg/mL) in Vero E6 cells (an African green monkey kidney cell line), with a CC of 4221 µg/mL, indicating a favorable selectivity index. Additionally, it exhibited strong activity against H1N1 in Madin-Darby canine kidney cell line (MDCK cells) (IC = 57.30 µg/mL, CC = 3073 µg/mL). Among all the extracts, the methanol extract showed the highest antiviral activity. It has IC = 2.549 µg/ml and selectivity index (SI) = 230 against H1N1.While it showed IC = 10.83 µg/ml against SARS-CoV-2 and 9.82 µg/ml against MERS-CoV with SI values of 54.2 and 59.77, respectively. Molecular docking studies revealed that 5-Methyl-5 H-naphtho[2,3-c]carbazole,7 H-Dibenzo[b, g]carbazole, 7-methyl, hesperidin, luteolin-7-glucoside-3'-glucuronide, Melitric acid A, and other compounds exhibited high binding affinities to the receptor-binding domains (RBDs) of SARS-CoV-2 and MERS-CoV spike glycoproteins, suggesting their potential to interfere with viral entry. Furthermore, GC-MS-identified bioactive compounds, including docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), paromomycin, and phenolic acids, demonstrated additional antiviral potential. These results underscore the potential of M. officinalis extracts as natural antiviral agents, offering a foundation for further in vitro and in vivo validation and potential therapeutic applications against respiratory viral infections, including coronaviruses and influenza viruses.