The applications of microalgae biomass have been widely studied worldwide. The classical processes used in outdoor cultivations of microalgae, in closed or open photobioreactors, occur in the presence of bacteria. Understanding how communication between cells occurs through quorum sensing and evaluating co-cultures allows the production of microalgae and cyanobacteria to be positively impacted by bacteria, in order to guarantee safety and profitability in the production process. In addition, the definition of the effects that occur during an interaction, promotes insights to improve the production of biomolecules, and to develop innovative products. This review presents the interactions between microalgae and bacteria, including compounds exchanges and communication, and addresses the development of new pharmaceutical, cosmetic and food bioproducts from microalgae based on these evaluations, such as prebiotics, vegan skincare products, antimicrobial compounds, and culture media with animal free protein for producing vaccines and other biopharmaceutical products. The use of microalgae as raw biomass or in biotechnological platforms is in line with the fulfillment of the 2030 Agenda related to the Sustainable Development Goals (SDGs).