Structure/function relationships of different biopolymers (alginate, dextran, or β-cyclodextrin) were analyzed as single excipients or combined with trehalose in relation to their efficiency as enzyme stabilizers in freeze-dried formulations and compared to trehalose. Particularly, a novel synthesized polymer β-cyclodextrin-branched alginate (β-CD-A) was employed as excipient. During freeze-drying, the polymers or their mixtures did not confer better protection to invertase compared to trehalose. β-CD-A (with or without trehalose), β-cyclodextrin (β-CD), or dextran with trehalose were the best protective agents during thermal treatment, while β-CD and alginate showed a negative effect on invertase activity preservation. The β-CD linked alginate combined the physical stability provided by alginate with the stabilization of hydrophobic regions of the enzyme provided by cyclodextrin. β-CD-A was effective even at conditions at which trehalose lost its protective effect. A relatively simple covalent combination of two biopolymers significantly affected their functionalities and, consequently, their interactions with proteins, modifying enzyme stability patterns.