The potential of nanotechnology revolutionized the different fields of modern sciences, enabling researchers to develop nanomaterial with extraordinary functionalities making life easier. Nanoparticles such as ZnO NPs and Ag NPs along with sterilizing agents found great potential for controlling contamination in banana tissue culture. Banana provides food for millions of people worldwide even though its origin was South East Asia and the Indian subcontinent. The emergence of tissue culture technology replaces the conventional banana propagation method, i.e., using suckers. Contaminations persist in tissue culture due to nutrient-rich media, thus decreasing its efficiency and profitability. The motive of this study is to make banana tissue culture more profitable by eradicating the contamination problem. Surface-sterilized explant may not be germ-free from inside due to covert bacteria (endogenous bacteria), which reside inside the plant in a passive state but can contaminate the experimental setup at later stages. In the present study, an experiment is designed by using various sterilizing agents (ethanol, NaOCl, H2O2, and HgCl2) for different periods to optimize the best combination of sterilizing agents for banana tissue culture. After treatment with these chemicals, the explant was inoculated to Murashige and Skoog (MS) media with plant growth hormones such as kinetin and indole acetic acid (IAA) and placed into a growth chamber for 1 week and observed regularly for appearance of contamination. The result shows that when the explant was treated with 70% ethanol for 1 min, 20% NaOCl for 10 min, and 0.2% HgCl2 for 2 min, we found it to be the most effective with the least contamination, i.e., 20%. In a separate experiment, zinc oxide (ZnO) and silver (Ag) nanoparticles were used to control endophytic contamination with different concentrations (60 mg/liter, 90 mg/liter, 120 mg/liter). Both nanoparticles show promising results in controlling endophytic contamination, but using silver nanoparticles as a part of media controls up to 100% contamination. Dual treatment of ZnO and Ag nanoparticles as sterilizing agents as an additional component of media successfully removes the contamination but becomes the major cause of tissue death in banana tissue culture. Chemical sterilization was good but not efficient as compared to the combination with nanoparticle application. Blends of chemicals and nanoparticles are effective against microbes not only from the surface but also from the inside of the plant, so using available nanoparticles with optimized concentration may open a new way in tissue culture technology. The result of this research explains the success of nanoparticles (Ag NPs and ZnO NPs) in controlling exo and endophytic contaminations in banana tissue culture, thus creating a unique way of banana explant sterilization.