Regeneration of multiple individual plantlets from a single cell or explant is one of the main aims of plant tissue culture. This field has a wide scope for production of pharmaceutical metabolites through suspensions, production of plantlets from plants which does not set seeds, production of viral free plants etc. The productions systems are brought down by the event of microbial contamination that is generally fungal, bacterial and viral in origin, which occurs at different levels. Controlling these check points brings out a reduction in the microbial hazards. Similarly following a sterile and strict protocol at different stages reduces the percentage of accidental contamination, which starts from the process of selection of explants to the stage before hardening. Traditional techniques like proper sterilization of explants and equipment, to the latest measures such as incorporation of biocide and nanoparticles have reduced the effects caused by the microbial pollutants. Proper knowledge about the mechanism of action and the concentration of the antimicrobial compounds are necessary as higher dosage could lead to deleterious effects to the plantlets grown under in vitro conditions. Optimized control measures are mandatory to reduce the contamination as well as the cost of production, which are vital to improve the standards of plant tissue culture industries.