Bioactive properties of bovine glycosylated caseinomacropeptide (gCMP) like antibacterial effects are reported to be closely associated with their structure in terms of attached glycans. Technological properties are also influenced by the carbohydrate side chains. However, during product manufacturing gCMP can be modified due to processing. Processing conditions, which influence the degree of glycosylation of gCMP lead to alterations of bioactivity and techno-functional properties of gCMP and accordingly gCMP-containing products. Hence, gCMP was studied for its glycan stability during heat treatment and storage under different pH values. Process stability (preservation of native protein structure in terms of attached glycans) was analysed by quantifying the release of the terminal carbohydrate, N-acetylneuraminic acid (Neu5Ac), from gCMP. The results clearly showed that the thermal stability of gCMP is strongly influenced by pH. When the pH was decreased from 7 to 2, reduced stability was found even at low heating temperatures. Minimal destabilisation effects were found at neutral pH. Similar observations were found during storage of gCMP. Neu5Ac was released after six days of storage, with a maximum release of 30% at pH 2. Acidic pH conditions were responsible for the hydrolysis of the glycans from the peptide backbone during heat treatment and storage.