Microglia physically contact a small population of synapses in the healthy adult brain; however, it has been shown that their interaction leads to the regulation of synaptic stability by either increasing or decreasing the volume and number of spines. These actions contribute to the formation, maturation, and plasticity of neural circuits, which ultimately shape animal behavior. In this study, we investigated the implications of hippocampal microglial depletion for the processing of spatial and aversive memories. To do this, we trained female rats in a spatial object recognition task and administered clodronate into the hippocampus to achieve local microglial depletion. Prior to this, we performed immunofluorescence to evaluate the time window and specificity of this depletor. On the third day after an acute administration of clodronate, a transient decrease in the number of microglial cells was observed, without significant changes in the number of astrocytes or neurons. Three days after drug infusion, rats can acquire spatial memory and express it in the short term; however, they fail to consolidate it. Ten days after clodronate administration, these animals successfully acquired and consolidated an aversive memory. Our results highlight the role of hippocampal microglia in the dynamic processes of memory.