Microglia, the resident immune cells of the brain, act along a spectrum to maintain CNS homeostasis, respond to perturbations, and control neuronal activity. Disentangling the molecular mechanisms of human microglia-neuron crosstalk remains challenging due to the context-dependent, dynamic nature of their interaction. We introduce MEA-LINK, a systems-approach leveraging natural variation to screen for immune modulators of neuronal activity. This multi-modal platform integrates human induced pluripotent stem cell (hiPSC) technology with micro-electrode array (MEA) recordings and proteomic analyses of secreted immune factors, allowing for longitudinal samples and correlations across modalities. We applied MEA-LINK to explore microglia-neuron interactions during development and hyperactivity challenges. We show that human microglia accelerate neuronal network development and rescue hyperactive network phenotypes. Linking the secretome adaptations to neuronal network activity variations, we identified CCL4 as a top candidate in microglia-mediated hyperactivity control. Then, we functionally validated the context-dependent role of microglial CCL4 to neuronal CCR5 signaling in human neuronal networks. Our findings support a neuron-specific function of chemokines and their receptors in the brain and provide a new perspective for immune signaling in neuronal hyperactivity control. The MEA-LINK platform thus offers a foundation for comprehensive, systematic studies of human microglia-neuron interactions.