Microglia have been shown to provide instructive cues during neuronal development. These cues can impact neural stem and/or progenitor proliferation, neuronal migration, cell death and cortical circuit wiring. Alterations in microglia’s instructive cues have been shown to impact brain development where dysregulation have been linked to neurodevelopmental disorders such as autism spectrum disorder and schizophrenia. What then regulates microglia development? Here, we demonstrate that this relationship between neurons and microglia is not unidirectional. Excitatory cells play a similar instructive role in microglia development during the first few weeks of mouse postnatal development. Our results showed that pyramidal cells can dynamically adjust microglia in nascent local circuits through changes in neuronal activity. Our findings reveal that early postnatal activity-dependent mechanisms establish the appropriate proportions of microglia to pyramidal cells in the cerebral cortex. Understanding how this bidirectional communication between pyramidal cells and microglia can influence each other’s development will provide insights as to how the brain is built.