Green synthesis of nanoparticles has gained prominence in recent years as a cost-effective and environmentally sustainable approach. This green nanotechnology has diverse applications, and their potential impact on cellular processes needs to be thoroughly examined via nanomaterials. One of the major challenges in this field is the alleviation of oxidative damage, cytotoxicity, and genotoxicity induced by nanoparticles. Lately, research is more focused on analyzing the epigenetic effects including DNA methylation and histone modifications mediated through the alteration in microRNA expression that is influenced by nanoparticles. Due to their physical and chemical properties, these nanomaterials are extremely suitable carriers of targeted modifications in gene regulatory systems. Delivery of silencing RNAs and artificial transcription factors built on nanoparticles for modulating gene expression has been extensively reported in recent years. Studies on various cell lines have confirmed the downstream effects of these changes in gene expression, as demonstrated by the significant alteration in expression of proteins functional in a multitude of pathways, such as those associated with oxidative stress, cytoskeletal proteins, molecular chaperones, proteins involved in energy metabolic processes, and apoptosis and tumor-related proteins. This reshuffling of molecular expression has also been corroborated by investigations at genomic, transcriptomic, proteomic, and metabolomic levels. This chapter highlights the detailed mechanism of modulation of gene regulation and expression, and the cytological and molecular changes caused by these bionanomaterials. The toxicological aspects and biocompatibility impacts of these nanoparticles, which are of paramount importance while considering their biomedical and environmental applications, have also been outlined.