Abstract Microglia, the immune cells of the brain, are a focus of studies in neurodegenerative diseases. Similarly, research about induced pluripotent stem cell (iPSC)-derived whole brain and region-specific organoids is increasing. In organoids, the complexity of the culture systems increases, mimicking better the actual scenario in the human brain. Furthermore, animal models do not always recapitulate human neurodegeneration, and they imply more ethical concerns compared to organoid systems. Recently the integration of iPSC-derived microglia into brain organoids has been achieved, and on-chip technologies have been focusing on microglia interaction with neural cells. In this review, we discuss the achievements on integrating microglia into brain organoids. We study the cell organization, ultrastructure and cell signalling of microglia with respect to other cell types in organoids as well as their functionality in the system. A particular focus here is on the interaction with the midbrain and dopaminergic systems. Finally, we discuss the achievements until now concerning neuroinflammation and disease modelling, and the possible therapeutic approaches targeting microglia and neuroinflammation in 3D systems.