C‐phycocyanin, a natural blue dye, stands out today because it has antioxidant, anti‐inflammatory, and anti‐tumor properties, and it can be extracted from cyanobacteria, such as the genus Spirulina. A process that has received attention is the adsorption of proteins in the presence of biomass by fluidized bed, particularly an expanded bed. Therefore, this study aimed at purifying C‐phycocyanin by ion exchange chromatography in expanded bed in the presence of biomass with two different resins (Streamline Q XL and Streamline DEAE) and comparing the purification process of C‐phycocyanin by applying the fixed bed ion exchange chromatography. The expanded bed purification carried out with the support of Streamline Q XL was considered more promising than with Streamline DEAE since the former had higher C‐phycocyanin recovery than the latter. The fraction C‐phycocyanin in the expanded bed mode with Streamline Q XL had average purity of 1.6, concentration of 2.4 mg mL−1, and recovery process of 79 %. Moreover, by comparison with the fixed bed, the recovery of C‐phycocyanin was higher in the expanded mode, even though both purity levels were similar. It has been shown that such crude feedstocks can be applied to the bed without prior clarification steps. As a result, the single‐step recovery process (clarification, capture, and purification) can be established, thus eliminating the centrifugation step, saving energy, and reducing the cost of the process.