Numerous complexation mechanisms have been explored to stabilize the blue pigment phycocyanin from Arthrospira platensis. However, previous studies have primarily focused on the application of various methods rather than delving into molecular interactions. This study compared the interactions of citrus pectins with a high degree of esterification and a low degree of esterification as well as lambda-carrageenan. The goal was to identify a molecule suitable for complexation that maintains stability against heating in terms of color and colloidal stability. Size measurements employing dynamic light scattering and static light scattering, as well as characterization of properties such as zeta potential, were performed for the various complexes. Moreover, the complexation mechanism was investigated by isothermal titration calorimetry and computational blind docking. Weak complexes were formed at neutral pH, driven by an entropy gain facilitated by hydrophobic interactions and van der Waals forces between non-polar groups. It seems that this step is essential in achieving structures with a core shell formation. A decrease in pH resulted in intensified complex formation driven by enhanced electrostatic interactions, leading to a shift in enthalpy from values between -4 and -23 kJ center dot mol(-1) to values between -15 and -25 kJ center dot mol(-1). Multiple binding sites were identified across the protein surfaces, primarily involving polar groups. Interactions with arginine were particularly significant, exhibiting 28 interaction counts compared to only 8 for threonine, despite threonine's greater prominence in the protein sequence. These interactions are thought to compete with interactions between allophycocyanin and c-phycocyanin subunits and protein chromophore interactions, resulting in a color shift. The study highlights the importance of selecting the appropriate biopolymer for optimal performance, considering the delicate balance between strong interactions and bulkiness to prevent complex precipitation.