Bacteria, yeast, and microalgae are sources of biomolecules such as enzymes, lipids, pigments, organic acids and, proteins for industrial application. These high-added-value biomolecules are often intracellularly bioaccumulated, and their recovery involves several downstream processes, in which the most crucial stage is the disruption of the cell wall. The choice of the method influences the further downstream steps and, consequently, its complexity and cost. In this review, severe and gentle methods currently used for disruption or permeabilization of bacteria, yeast, and microalgae were discussed based on their principle, application, and feasibility. Also, recent studies regarding the microbial cell disruption were presented in order to facilitate the choice of the more effective method. Some factors such as cell wall composition, nature of biomolecule, purity degree, scalability, and energy input are necessary to be considered on selecting the most appropriate disruption method. The severe methods, such as high pressure-homogenization, and ultrasonication present higher yield, lower cost, and feasibility to scale-up when compared to the gentle methods. However, in order to achieve a higher recovery yield, further studies must focus on the optimization of operational parameters and on the combination of severe and gentle methods.