Introduction <p>Therapeutic proteins are crucial in the treatment of a wide range of diseases. However, the proteins are sensitive to chemical degradation reactions, particularly deamidation and isomerization, which can compromise efficacy and safety. Formulation excipients, such as sugars and non-ionic surfactants, are commonly used to enhance stability, yet their effects on chemical degradation remain insufficiently understood.</p> Methods <p>This study investigates how fructose, sucrose, melezitose, and the non-ionic surfactants polysorbate 80 and DDM (n-Dodecyl-β-D-maltoside) affect the structure and chemical stability of the affibody GA-Z, a protein prone to deamidation and isomerization. Chemical degradation and conformational changes were characterized using peptide fingerprinting, Liquid Chromatography-Mass Spectrometry, Titration fluorescence spectroscopy, two-dimensional Nuclear Magnetic Resonance spectroscopy, and Differential Scanning Calorimetry.</p> Results <p>All three sugars lowered chemical degradation by stabilizing the folded state of the z-domain and inducing minor structural changes in the albumin-binding domain, thereby lowering the propensity for deamidation and isomerization. Polysorbate 80 showed minimal impact on both degradation and protein structure. In contrast, DDM increased deamidation and isomerization due to surfactant–protein interactions, resulting in structural changes.</p> Conclusion <p>These results demonstrate how excipient-induced structural changes affect chemical degradation of proteins in liquid formulations. This study contributes to the understanding and design of more effective formulations for therapeutic proteins, enhancing their stability and safety.</p> Graphical Abstract <p></p>