Affinity enrichment coupled with liquid chromatography–tandem mass spectrometry (AE–LC–MS/MS) enables a comprehensive study of virus–host protein–protein interactions in cells and tissues infected with Rift Valley fever virus (RVFV) or ectopically expressing RVFV proteins. Depending on the research question, different experimental setups with carefully chosen controls are needed. Here, we describe the detailed workflow of sample preparation, processing, and cleanup, while also outlining critical points to consider when designing and performing AE–LC–MS/MS experiments.