Browning and contamination are regarded as the main constraints in the plant tissue culture of Musa spp. that can hinder the success of plant propagation in vitro. Browning is caused by enzymatic reactions due to explant injury, while microbial contamination is caused by phyllospheric, rhizospheric, and endophytic microorganisms that reside on, in, and inside the plants. When not properly addressed, they can cause decreased regenerative ability, decreased callus growth, inhibited adventitious shoot growth, and even tissue death. To overcome the browning problem, various attempts have been made in vitro, e.g., immersing the explants in an anti-browning solution, incorporating anti-browning compounds into the medium, and manipulating cultural practices. Correspondingly, to control the problem of contamination, efforts have been made, for example, using various methods, such as thermotherapy, chemotherapy, and cryotherapy, and chemical agents, such as disinfectants, antiseptics, and nanoparticles. This review aims to investigate and provide a comprehensive understanding of the causes of browning and contamination as well as the many approaches used to control browning and contamination problems in Musa spp. tissue cultures.