Influenza A viruses are responsible for the annual epidemics that cause severe illness in millions of people worldwide. Seasonal vaccines are administered to prevent infection but the two major antigenic glycoproteins found on the viral surface, hemagglutinin and neuraminidase, for which there are numerous subtypes, are subject to continual antigenic change. Protective immunity is only conferred when there is antigenic similarity between the strains used for vaccine development and circulating influenza isolates. Insights into influenza biology and host responses to viral infection are therefore needed to guide new effective therapeutics and vaccines. Proteomic profiling has highlighted changes in host-cell responses to influenza infection that are strain-specific and related to pathogenicity, however the dynamics of the host and viral glycoproteomes during infection have not been taken into consideration. Glycosylation is an essential regulatory mechanism of protein function and can have a profound influence on both normal and irregular biological processes. The importance of glycosylation in host-pathogen interactions is well established, viral surface proteins have been implicated attachment and entry, induction of immune responses and evasion of host-immune defences. Influenza must subvert host glycosylation machinery to synthesise the biomolecules required for productive infection, and in doing so, the virus disrupts these host pathways. We studied the glycoproteome and proteome of adenocarcinomic human alveolar basal epithelial cells during influenza infection. For the proteomic analyses, we implemented a SWATH approach to quantify changes in proteins from subcellular fractions. This revealed increased membrane lipid metabolism, clathrin-dependent endocytosis and cytokine signaling during viral infection. For the glycoproteomic analyses we enriched glycopeptides by HILIC from subcellular fractions and investigated the monosaccharide composition of the attached glycans in a site-specific manner using ByonicTM software. The work presented herein highlights site-specific changes in host protein glycosylation, including decreased sialylation and increased fucosylation in influenza infected cells.