In the food industry, the phycobiliprotein phycocyanin acts as a color pigment or the functional part of the superfood “Spirulina.” It is industrially extracted from Arthrospira platensis. Current scientific research is focusing on finding complex partners with the potential to stabilize phycocyanin against its sensitivity toward heating and pH changes. Less attention is paid to the factors that influence complexation. This study focuses on the mixing ratio of phycocyanin with pectin. Phycocyanin concentration was fixed, and the mixing ratios ranged from 0.67 to 2.50 (pectin:phycocyanin). All samples were analyzed for their color, size, microscopic structure, zeta potential, and sedimentation stability before and after heating at 85°C. It was found that increasing the pectin content fostered the initial interactions with the protein and chromophore, resulting in a color shift from blue to turquoise. The size of the complexes decreased from several micrometers to nanometers with increasing pectin concentration. Those smaller complexes that were formed at a mixing ratio of 2.5 showed a higher colloidal stability over a period of ∼2 days. It is suggested that at a low mixing ratio (0.67), phycocyanin cannot be completely entrapped within the complexes and attaches to the complex surface as well. This results in aggregation and precipitation of the complexes upon heating. With increasing aggregation and consequently size as well as density of the complexes, sedimentation was accelerated.Practical ApplicationUnder acidic conditions, as found in many foods and beverages (e.g., soft drinks, hard candy), phycocyanin tends to agglomerate and lose its color. Specifically heating, triggers denaturation, causing phycocyanin to aggregate and lose vital protein–chromophore interactions necessary to maintain a blue color. To prevent precipitation of the phycocyanin‐pectin complexes, increasing the amount of pectin to a ratio of at least 2.0 is effective. This illustrates how adjusting the mixing ratio improves stability. Conversely, lower mixing ratios induce color precipitation, valuable in purification processes. Thus, practical use of biopolymer‐complexes, requires determination of the optimal mixing ratio for the desired effect.