Bioorthogonal non-canonical amino acid tagging (BONCAT)-based approaches enable selective labeling of newly synthesized proteins (NSPs). We developed a workflow termed the “Phos-tag Click Tip” by integrating a phosphorylated variant of bicyclononyne (pBCN) with Phos-tag affinity purification to selectively capture azidohomoalanine (AHA)-labeled peptides. Applying this workflow, we performed comprehensive NSP profiling of host cells during influenza A virus (IAV) infection. We identified dynamic changes in NSP profiles associated with viral replication, host restriction, and immune responses, many of which were not readily detected by conventional whole-cell or phosphoproteomic analyses.