Major depressive disorder (MDD) is a common disease of the central nervous system that leads to high socio-economic and clinical challenges. Chronic stress is suggested to be a major risk factor for the disease, but little is known about the underlying mechanisms. Accumulating studies suggest that microglia are implicated in synaptic dysfunction that plays a crucial role in the etiology and course of depression. Here, we focus on the role of hippocampal microglia-synapse interaction during both the induction and remission after stress in a mouse model. Over a course of six weeks, we phenotype a depression-like mouse model by behaviorally inducing chronic mild stress to adult male mice in the automated IntelliCage system. During the remission paradigm, we assess the effect of an enriched environment on remission from stress. Simultaneously, we monitor structural changes of dendritic spines and microglia in the hippocampus using chronic in vivo two-photon microscopy. To address, whether microglia are necessary for changes in spine density or behavior, we deplete them via the CSF1-R antagonist BLZ945. Stress led to an increased spine density on hippocampal CA1 neurons that was dependent on the presence of microglia. As previously shown, enriched environment resulted in increased spine density and was able to ameliorate stress-dependent behavior phenotypes. Surprisingly, enriched environment related dendritic spine increase was independent of microglia, since BLZ945 depletion of microglia did not affect the enriched environment related spine density increase. Analysis of microglia process motility showed no changes upon stress induction. However, enriched environment exposure correlated with an increased microglia fine processes’ motility. Our multimodal approach of simultaneous and chronic in vivo imaging in combination with microglia motility and dendritic spine density measurements in behaving mice enabled us, to investigate the relationship of dendritic spine changes and microglia under stress conditions in the hippocampus.