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Direct laser writing (DLW) is a three-dimensional (3D) manufacturing technology that offers vast architectural control at submicron scales, yet remains limited in cases that demand microstructures comprising more than one material. Here we present an accessible microfluidic multi-material DLW (μFMM-DLW) strategy that enables 3D nanostructured components to be printed with average material registration accuracies of 100 ± 70 nm (ΔX) and 190 ± 170 nm (ΔY) – a significant improvement versus conventional multi-material DLW methods. Results for printing 3D microstructures with up to five materials suggest that μFMM-DLW can be utilized in applications that demand geometrically complex, multi-material microsystems, such as for photonics, meta-materials, and 3D cell biology.