Glycosylation is a critical quality attribute (CQA) that can impact on product safety and efficacy of protein biopharmaceuticals. Characterization of N-glycans is therefore of paramount importance for the pharmaceutical industry. Hydrophilic interaction liquid chromatography (HILIC) combined with fluorescence detection (FLD) and 2-aminobenzamide (2-AB) labelling is the golden standard for the analysis of N-glycans enzymatically liberated from biopharmaceuticals. However, for phosphorylated N-glycans, that is, those attached on lysosomal enzymes, irreproducible data and recovery issues are observed on conventional liquid chromatography (LC) instrumentation and columns, which can be attributed to the interaction of the phosphate moieties with stainless steel components in the flow path. This article demonstrates the analysis of phosphorylated glycans with full recovery on a bio-inert LC system and PEEK-lined HILIC column.