ABSTRACT Persistent HIV-1 infection in cells of the monocyte/macrophage lineage in tissues such as the brain, gut, lymphoid tissues, or adipose tissue forms an under-investigated viral reservoirs that will prevent eradication of HIV-1, even if the reservoir in CD4+ T cells could be addressed. However, other than for latently HIV-1 infected T cells, so far the biomolecular control of latency in myeloid cells has not been detailed. We demonstrate that latently HIV- 1 infected monocyte/macrophages transition from a normal 2n chromosome set to a 4n chromosome state. This is consistent with a previous report that describes the transition of the most active macrophages combating Mycobacterium tuberculosis infection to a polyploid state, indicating that 4n transition is a natural mechanism of macrophages during their pathogen response. Polyploidy is not only known to increase resistance to many challenges that would otherwise result in cell death, but also triggers non-linear transcriptomic effects, which disrupt proper cell signaling and we propose are part of the inability of HIV-1 to establish active infection. Non- linear transcriptomic effects become obvious in the comparison of genome-wide transcriptomic signatures (RNA- seq) of different latently HIV- 1 infected monocyte clones, which show extensive inter-clonal heterogeneity. However, despite this extensive transcriptomic heterogeneity, latently HIV-1 infected macrophages share a small common altered biomolecular signature at the transcriptome (RNA-seq) and proteome level (kinome analysis). We identified the phosphatase PPM1A as a key element of this latency control signature. Modulation of PPM1A expression controlled active HIV-1 infection in macrophages, regulated the susceptibility of macrophages to HIV- 1 induced cell death, and altered the capacity of myeloid cells to establish latent infection. Thus targeting PPM1A has the potential to provide a new therapeutic avenue to eradicate HIV-1 reservoirs in macrophages. This application will contribute to our basic molecular understanding of how the intrinsic antiviral response of myeloid cells is controlled and how therapeutic modulation of PPM1A activity could contribute to the elimination of persistent HIV-1 reservoirs in myeloid cells in general and specifically in brain-resident microglia.