Cold atmospheric plasma (CAP) is a specific type of partially ionized gas that is less than 104°F at the point of application. It was recently shown that CAP can be used for decontamination and sterilization, as well as anti-cancer treatment. Here, we investigated the effects of CAP on HIV-1 replication in monocyte-derived macrophages (MDM). We demonstrate that pre-treatment of MDM with CAP reduced levels of CD4 and CCR5, inhibiting virus-cell fusion, viral reverse transcription and integration. In addition, CAP pre-treatment affected cellular factors required for post-entry events, as replication of VSV-G-pseudotyped HIV-1, which by-passes HIV receptor-mediated fusion at the plasma membrane during entry, was also inhibited. Interestingly, virus particles produced by CAP-treated cells had reduced infectivity, suggesting that the inhibitory effect of CAP extended to the second cycle of infection. These results demonstrate that anti-HIV activity of CAP involves the effects on target cells and the virus, and suggest that CAP may be considered for potential application as an anti-HIV treatment.