Early life stress (ELS), a prenatal/early postnatal period of severe trauma, social deprivation, or neglect, among other adversities, constitutes a risk factor for developing psychopathologies and different health complications in adulthood. Maternal separation with early weaning (MSEW) induces long-term consequences in mouse retinal function and structure. We analyzed microglia involvement in adult retina ELS-induced sequelae. C57Bl/6 J mice were separated from the dams at postnatal days (PND) 4-6, 7-9, 10-12, and 13-16, for 2 h, 3 h, 4 h, and 6 h, respectively, and were weaned at PND 17. Control pups were left undisturbed and weaned at PND 21. At PND 45, MSEW induced microgliosis and decreased retinal ganglion cell (RGC) function, followed by RGC loss at PND 60. Microglial phenotypic alterations correlated with a pro-inflammatory profile (i.e., increase in the nuclear levels of nuclear factor kappa B -subunit p65, and C3-, nitric oxide synthase-2, and interleukin-1β-immunoreactivity in Iba-1 ( +) cells). Depleting microglia between PND 35 and 60 did not affect the retina from naïve mice. However, in early stressed mice, it preserved RGC function and number, visually mediated behavior, and contrast sensitivity. Therefore, microglial reactivity could be one of the key factors linking progressive alterations provoked by ELS in adult mice retinal function and structure.