HIV-1 infection induces a chronic inflammatory environment not restored by suppressive antiretroviral therapy (ART). As of today, the effect of viral suppression and immune reconstitution in people living with HIV-1 (PLWH) on long-term suppressive ART (PLWHART) is not well-described. Herein, we show how PLWH who naturally control the virus (PLWHEC) have a reduced proportion of CD4+CCR6+ cells compared to PLWHART and HIV-1 negative controls. Specifically, the CD4+CCR6+/CCR6- cells exhibited a uniqe proteomic profile with a modulated energy metabolism in PLWHEC compared to PLWHART independent of CCR6 status. Furthermore, the CD4+CCR6+ cells were enriched in proteins involved in apoptosis and p53 signalling in PLWHEC compared to PLWHART, indicative of increased sensitivity towards cell death mechanisms. Collectively, this data shows how PLWHEC have a unique chemokine receptor profile that may aid in facilitating natural control of HIV-1 infection.