Background Colorectal cancer (CRC) is the third most prevalent form of cancer and fourth leading cause of morbidity worldwide. Surgical resection remains the only curative approach for CRC, but recurrence following surgery is the main problem and ultimate cause of death. Lycopodium clavatum and quercetin have been found to exert its anticancer properties. The aim of the present study is to investigate whether quercetin or L. clavatum extract and combination of both have any profound role in reducing major inflammatory cytokines in Colo-320 cells. Methods L. clavatum and Quercetin alone or in combination was administered to colon cancer cells and various toxicity markers, gene expression analyses of apototic genes and gelatin zymmography were performed. Results Quercetin (50 μm) in combination with L. clavatum extract (10 μL) distinctly reduced cell growth and highlighted their potential effects in extirpation of colon cancer cells. Treatment with increased dose of L. clavatum extract in combination with quercetin reduced the colony size and proliferation potential when compared to the sole treatment of plant extracts. In the antimicrobial assays, it was observed that Lycopodium alone exhibited antimicrobial activity against Escherichia coli and Pseudomonas aeruginosa. Characterization of L. clavatum extract and quercetin was performed and confirmed the presence of flavonoids and alkaloids. Treatment with Lycopodium and quercetin combination induced significant down-regulation in activities of MMP2 and MMP9 tested by gelatin zymography. The combined treatment greatly affected the mRNA expression of p53, Bcl2, Bax, Caspase 3, Wnt 1, Cyclin D1, and Catalase genes in colon cancer cells. Conclusion The synergistic effect between Lycopodium and quercetin might bring forward the enhanced antitumorigenic properties of combinational therapy with natural products to successfully combat the cancer progression with minimal side effects and resistance to drugs.