This review presents a balanced synthesis of the efficacy–nanotoxicity window of nanomaterials—including carbon-based structures, metallic nanoparticles, and bioceramic composites—within the context of stem cell–assisted tissue engineering. It emphasizes that increases in conventional differentiation markers may not necessarily correspond to functional maturity or long-term safety. Therefore, a gradual shift from standard viability-based assays toward lineage-specific functional assessments is discussed. The nanotoxicological profile of these materials is examined across major tissue types, highlighting how similar physicochemical properties may yield beneficial or adverse outcomes depending on concentration, exposure time, and microenvironmental conditions. In bone tissue, the review considers the point at which enhanced mineralization may be accompanied by oxidative stress and mitochondrial strain. For cartilage, potential concerns related to ion and degradation product accumulation in avascular environments are addressed, including the possible induction of inflammatory signaling and hypertrophic markers such as collagen type X. In neural and cardiac applications, efforts to improve electrical conductivity are evaluated alongside potential electrophysiological alterations, including Ca2+ imbalance and rhythm disturbances at sub-cytotoxic levels. Vascular differentiation is discussed within the context of pro-angiogenic signaling and the risk of endothelial dysfunction. By comparing experimental systems ranging from 2D cultures to induced pluripotent stem cell (iPSC)–derived organoids, the review underscores the model-dependent and tissue-specific nature of nanotoxic responses. Overall, it outlines considerations for integrating physicochemical characterization with functional and metabolic endpoints to support more reliable evaluation of nanobiomaterials in regenerative medicine.