Microglia are immune cells in the brain that survey the brain parenchyma and transiently contact synapses. Their physiological roles at synapses are not well understood. This study investigated microglial interactions with synapses during normal and altered sensory experience in the visual cortex of juvenile mice. During normal visual experience, microglial processes directly apposed multiple synapse-associated elements, including synaptic clefts, and were surrounded by pockets of extracellular space. In terms of dynamics, microglial processes localized to the vicinity of small and transiently growing dendritic spines, which typically lost over 2 days. When experience was manipulated through light deprivation and reexposure, microglial processes changed morphology, showed altered extracellular space distribution, displayed phagocytic structures, apposed synaptic clefts more frequently, and enveloped synapse-associated elements more extensively. Light deprivation caused microglia to become less motile and change their preference for localization to a subset of larger dendritic spines that persistently shrank, while light reexposure reversed these behaviors. These findings suggest that microglia may actively contribute to experience-dependent modification or elimination of a subset of synapses in the healthy brain. Microglial interactions with synapses are subtly altered by sensory experience, indicating that microglia are not only activated during early brain development or pathological conditions but also change their behavior toward synapses in response to sensory experience. This raises the possibility that microglia may contribute to fine-tuning the plastic capacities of individual synapses in the healthy brain. The study used immunocytochemical electron microscopy, serial section electron microscopy with three-dimensional reconstructions, and two-photon in vivo imaging to characterize microglial interactions with synapses during normal and altered sensory experience. The findings reveal different modalities of microglial interactions with synapses that are subtly altered by sensory experience. These findings suggest that microglia may actively contribute to the experience-dependent modification or elimination of a specific subset of synapses in the healthy brain.Microglia are immune cells in the brain that survey the brain parenchyma and transiently contact synapses. Their physiological roles at synapses are not well understood. This study investigated microglial interactions with synapses during normal and altered sensory experience in the visual cortex of juvenile mice. During normal visual experience, microglial processes directly apposed multiple synapse-associated elements, including synaptic clefts, and were surrounded by pockets of extracellular space. In terms of dynamics, microglial processes localized to the vicinity of small and transiently growing dendritic spines, which typically lost over 2 days. When experience was manipulated through light deprivation and reexposure, microglial processes changed morphology, showed altered extracellular space distribution, displayed phagocytic structures, apposed synaptic clefts more frequently, and enveloped synapse-associated elements more extensively. Light deprivation caused microglia to become less motile and change their preference for localization to a subset of larger dendritic spines that persistently shrank, while light reexposure reversed these behaviors. These findings suggest that microglia may actively contribute to experience-dependent modification or elimination of a subset of synapses in the healthy brain. Microglial interactions with synapses are subtly altered by sensory experience, indicating that microglia are not only activated during early brain development or pathological conditions but also change their behavior toward synapses in response to sensory experience. This raises the possibility that microglia may contribute to fine-tuning the plastic capacities of individual synapses in the healthy brain. The study used immunocytochemical electron microscopy, serial section electron microscopy with three-dimensional reconstructions, and two-photon in vivo imaging to characterize microglial interactions with synapses during normal and altered sensory experience. The findings reveal different modalities of microglial interactions with synapses that are subtly altered by sensory experience. These findings suggest that microglia may actively contribute to the experience-dependent modification or elimination of a specific subset of synapses in the healthy brain.