Polyelectrolyte multilayers (PEMs) based on biopolyelectrolytes are highly appealing for the surface engineering of biomaterials and the tuning of cell response and phenotypes for biomedical applications. However, cell adhesion is limited on biopolyelectrolyte PEMs. Thermal annealing provides a simple means to increase or decrease cell adhesion on PEMs. The work presented here aims to understand cellular interactions with annealed PEMs based on the adsorption and exchangeability of two model proteins: fibronectin (FN), an adhesion protein, and bovine serum albumin (BSA), a nonadhesion protein. Protein adsorption and exchangeability are studied on annealed poly‐l‐lysine (PLL)/sodium alginate (Alg) and chitosan (Chi)/hyaluronic acid (HA) PEMs using [131I] radiolabeled proteins and gamma counting. Upon annealing cell adhesion is enhanced on PLL/Alg multilayers and decreased on Chi/HA multilayers. For PLL/Alg PEMs, annealing increases adsorption of both FN and BSA and reduces exchangeability. For Chi/HA multilayers, annealing increases BSA adsorption but decreases FN deposition, accompanied by a greater exchangeability. Changes in topographic features of deposited proteins on annealed PLL/Alg hint on changes in the 3D structure of the proteins. Circular dichroism shows that FN retains a large β‐sheet contribution upon adsorption to both annealed and unannealed PLL/Alg PEMs, also suggesting changes in tertiary structure.