Plant genetic engineering is a potential tool for the improvement of plants for productivity, stress tolerance, and climate resilience. Conventional plant genetic engineering methods of gene transfer such as Agrobacterium-facilitated, gene gun, electroporation, viral transfection, and PEG-mediated transfection have several limitations. Organelle-targeted nanoparticle-based gene transfer in plants shows huge potential in plant transformation through genetic engineering for their sustainability and resilience. Nanoparticles may impact plants both positively and negatively, and promote plant growth and development through precise delivery, enhanced protection of genetic materials, uptake of nutrient elements, stable transfer of genes, phytoremediation, and stress tolerance. Nanoparticle-based plant genetic engineering enables plant trait improvement, enhanced stress tolerance, production of new biomolecules, environmental remediation, etc. This chapter discusses the application of nanoparticles in organelle organelle-targeted delivery of genetic materials into plants focusing on methods, advantages, applications, and challenges of this approach.