The biorefinery concept, specifically the third generation, arrives to proposing the microalgae and cyanobacteria biomass as a source of high added-value compounds such as proteins, pigments, carbohydrates, and lipids, between others for different industry applications. Within this framework, phycocyanin is a proteic pigment which is already competitive in the market due to its intense blue and fluorescent properties to be utilized in the color engineering also providing great health benefits. In this sense, the protein is directly linked to phycocyanin due to the presence of a blue-colored prosthetic group called phycobilin and this prosthetic group binds to the protein to form the complete phycocyanin. However, it is important to deepen the design to improve the process and thus increase yields in obtaining microalgal biomass. One of the great alternatives to above is the bubble column photobioreactors; these are broadly referred to as “bubbling” because they use a bubbling system to supply gases to the culture and at the same time promote mixing, and the column refers to the vertical shape of the photobioreactor; finally, it is important to highlight that the yields of the compounds obtained from microalgae species depend on inducing stress and adapting certain cultivation strategies. In this way, the objective of this chapter is to compile the most recent information about configurations parameters such as the air flow, temperature, bubble size, and light intensity to the production in industrial scale in bubble column photobioreactors to obtention of phycocyanin and protein from cyanobacterial and microalgal biomass.