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Microinjection protocols that involve using a hollow, high-aspect-ratio microneedle to deliver foreign material (e.g., cells, DNA, viruses, and micro/nanoparticles) into biological targets (e.g., embryos, tissues, and organisms) are essential to diverse biomedical applications in both research and clinical settings. A key deficit of such protocols, however, is that standard microneedle architectures are inherently susceptible to clogging-induced failure modes, which can diminish experimental rigor and lead to failed microinjections. Additive manufacturing (or “three-dimensional (3D) printing”) strategies based on “Two-Photon Direct Laser Writing (DLW)” offer a promising route to address clogging failure phenomena by rearchitecting the needle tip, yet achieving 3D-printed microneedles with the mechanical strength necessary to penetrate into biological targets (e.g., embryos) has remained a critical barrier to efficacy. To overcome this barrier, here we harness a recently reported polyhedral oligomeric silsequioxane (POSS) photomaterial to DLW-print fused silica glass high-aspect-ratio microinjection needles with enhanced mechanical strength. Experimental results for POSS-based 3D-nanoprinted microneedles with inner and outer diameters of 10 μm and 15 μm, respectively, and heights ranging from 500–750 μm revealed that the needles not only enabled successful puncture and penetration into early-stage zebrafish embryos, but also significantly reduced the magnitude of undesired deformations to the embryos during needle puncture and penetration from 61.0±12.1 μm for standard glass-pulled control microneedles to 42.4±11.5 μm for the POSS-enabled 3D microneedles (p < 0.01). In combination, these results suggest that wide-ranging biomedical fields could benefit from the presented 3D microinjection needles.