The growing use of engineered nanomaterials in both commercial products and biomedical applications leads to increasing exposure for production line workers, consumers and patients. Therefore, the understanding of biological effects induced by nanomaterials is crucial for their safety assessment. An important group of nanomaterials is represented by metal(loid)-based nanoparticles, because of their unique physico-chemical properties. Metal(loid)-based nanoparticles themselves, the related ion release, and their nanometallomes, can potentially interact with essential elements causing dys-homeostasis and adverse biological effects. In this work, we describe the effects of metal(loid)-based nanoparticles on essential element homeostasis. In particular, we consider the most used and promising metal(loid)-based nanoparticles, highlighting that the new emerging concept of nanometallomics is important to disclose the impact of these nanoparticles on human health and the related long-term effects.