HIV-1 Elite controllers (EC) are a rare group among HIV-1-infected individuals who can naturally control viral replication for a prolonged period. Due to their heterogeneous nature, no universal mechanism could be attributed to the EC status; instead, several host and viral factors are discussed for playing a role. In this study, we investigated the fecal metabolome and microbiome in a Swedish cohort of EC, treatment-naïve viremic progressors (VP) and HIV-negative individuals (HC). We observed an enrichment of dipeptides in EC compared to the other two study groups. In vitro analyses identified anti-HIV-1 properties for two dipeptides that could bind to the HIV-1 gp120. Furthermore, these dipeptides supported bacterial growth of the genus Prevotella in vitro that was enriched in EC, which influences host metabolism. Thus, increased levels of both dipeptides and Prevotella could provide beneficial effects for EC. These findings open new possibilities to develop therapeutics against HIV-1.