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 in protein biosynthesis, 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 at time points during influenza infection to try and identify novel pathways that can be exploited as targets for therapeutics. For the glycoproteomic analyses we enriched glycopeptides by HILIC from subcellular fractions and investigated site-specific occupancy and the monosaccharide composition of the attached glycans. For the proteomic analyses, we implemented a SWATH approach to quantify changes in proteins from subcellular fractions. The work presented herein highlights the these mass spectral approaches to monitor the dynamic glycoproteome and proteome during influenza infection.