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Summary Multiple protocols have been published for generation of iMGLs from hESCs/iPSCs. To date, there are no guides to assist researchers to determine the most appropriate methodology for microglial studies. To establish a framework to facilitate future microglial studies, we first performed a comparative transcriptional analysis between iMGLs derived using three published datasets, which allowed us to establish the baseline protocol that is most representative of bona fide human microglia. Secondly, using CRISPR to tag the classic microglial marker CX3CR1 with nanoluciferase and tdTomato, we generated and functionally validated a reporter ESC line. Finally, using this cell line, we demonstrated that co-culture of iMGL precursors with human glia and neurons enhanced transcriptional resemblance of iMGLs to ex vivo microglia. Together, our comprehensive molecular analysis and reporter cell line are a useful resource for neurobiologists seeking to use iMGLs for disease modeling and drug screening studies., Highlights • Integrated molecular characterization reveals differences in four iMGL protocols • A dual tdTomato and nanoluciferase reporter tool was generated to track iMGLs via CX3CR1 • Kinetics of surface marker expression during iMGL differentiation • Co-culture with glia/neurons restores ex vivo microglial transcription factors, In this article, Jose Polo and colleagues molecularly compare existing microglia differentiation methods from stem cells, generate a new dual fluorescent and enzymatic reporter tool to study microglia, and show that human glia/neuron co-culture pushes the regulatory landscape of in vitro microglia-like cells to more closely resemble bona fide microglia.