Cellular and tissue organization depends on the spatial arrangement, ultrastructure, and functional coupling of organelles. This review reframes intracellular nanomaterials as nanoscale tools for interrogating and modulating membrane contact sites (MCSs), rather than simply as delivery systems. We focus on mitochondria, the endoplasmic reticulum, lysosomes, endosomes, and the nucleus because these compartments form dynamic contact networks that regulate metabolism, calcium and redox signaling, membrane trafficking, autophagy, mitophagy, chromatin organization, stress adaptation, and cell fate. Emphasis is placed on morphological and ultrastructural readouts, including mitochondrial cristae organization, fission-fusion balance, membrane-potential-dependent localization, endosomal and lysosomal trafficking, ER-mitochondria and lysosome-mitochondria communication, nuclear-pore access, chromatin organization, and inter-organelle contact-site remodeling. We discuss how particle size, surface charge, geometry, ligand presentation, and stimulus-responsive behavior influence cellular uptake, endosomal escape, organelle localization, and structural consequences within cells and tissues. A central distinction is made between intentional organelle nano-regulation, in which engineered systems are designed to engage defined subcellular mechanisms and organelle interfaces, and incidental stress responses, in which altered morphology or gene expression reflects oxidative, lysosomal, mitochondrial, inflammatory, or genotoxic injury. By organizing current evidence around MCS biology, subcellular compartmentalization, membrane trafficking, organelle dynamics, and tissue-relevant cell fate decisions, this review provides a morphology-centered framework for evaluating intracellular nanomaterials in health, disease, stem-cell biology, and regenerative bioengineering.
