The current article will review the efficient and recent technologies for controlling the microbial contaminants at plant tissue culture stages. Several sources can originate contamination in plant tissue culture such as mother plants, surface sterilization, and in vitro contamination by bacteria and fungi. Explant contamination results from donor plants as well as environmental factors such as surface sterilization, age, size, and source of the explants, as well as explants kept under stringent sanitary conditions. Many issues in the greenhouse come to an end if robust branches with functioning leaves are developed during the establishment stages. During the establishment stages, chemicals like H2O2, AgNO3, Ca(ClO2), and HgCl2 also showed good results for the surface sterilization of some fruit trees. Reducing contaminations can help explain this, and it also depends on the kind of tissue and the type of explant being utilized for micropropagation. Both Carbenicillin and Cefotaxine, when used alone or in combination, are the most effective antibiotics against bacterial contamination in plant tissue culture. Recently, nanomaterials as modern agriculture sector was applied to solve microbial contamination problems, such as using nanochitosan and nanosilver to control total microbes.