The effect of β-cyclodextrin modifications (polymerization (PCD) and later carboxymethylation (CMPCD)) on their action as enzyme stabilizers was analyzed during freeze-drying and thermal treatment. Combined polymer-trehalose matrices were also employed. Due to their higher T_g values, PCD and CMPCD provided better structural stability to the freeze-dried formulations than β-CD. However, only PCD was a good excipient to protect invertase both in amorphous and supercooled systems. FT-IR revealed increased protein denaturation in the presence of CMPCD, but not in the presence of PCD. Even though all polymers inhibited/delayed trehalose crystallization, only trehalose (T) combined with PCD (PCD + T) and with β-cyclodextrin (β-CD + T) offered the best stability to the enzyme. In β-CD + T system, trehalose was the main responsible for the protection. In PCD + T system, both additives contributed to improve the enzyme stability. FT-IR and DSC were useful to analyze the combined role of molecular and supramolecular interactions on enzyme stability in dehydrated model systems.