Human endogenous retroviruses (HERVs) are the result of an ancient retroviral infection that integrated into the human genome millions of years ago. Since then, HERVs have undergone multiple transposition events and as a result now comprise up to 8% of the human genome. Some HERVs have maintained a complete proviral structure, comprising gag, pro, pol and env genes flanked by two long terminal repeats. Despite previously being considered junk DNA, recent studies have shown that HERVs are being actively expressed in healthy human tissue, indicating that they may play a role in the diversity of the human proteome and can impact human health and disease. However, the mechanisms by which HERV proteins interact with the cellular machinery are not well known and are challenging to explore, owing to the complex nature of viral protein production. Specifically, the HERV polyproteins Gag, Gag–Pro and Gag–Pro–Pol are produced by two -1 ribosomal frame shifts making them challenging to fuse with traditional proximity labelling enzymes. Here, we report the development of an ALFA-tagged expression system for HERV Gag, Pro, Pol and Env amenable to TurboID proximity labelling. We demonstrate the ability of this system to direct proximity labelling to the ALFA-tagged proteins of interest and leverage this system to uncover the interactome of four HERV polyproteins. This knowledge is an important advance in our fundamental understanding of human biology, and mapping the cellular footprint of the HERV polyproteins is a crucial next step that will support future therapeutic development.