Nano-enabled approach has become the promising option for resolving heavy metal (HMs) contamination and improving the crop production. Here, current study explored mechanism involved in how green silicon nanoparticles (SiNPs) alleviating the chromium (Cr) induced toxicity in tomato. Green SiNPs in spherical shape with size 8–40 nm were synthesized with artemisia annua leaves extract and characterization performed by modern characterization method. The results of the green house experiment demonstrated that SiNPs at dose of 150 mg kg−1 surprisingly improved the biomass and root architecture of tomato plants. SiNPs supplementation also positively enhanced the photosynthesis pigments and leaf gas exchange attributes of Cr-stressed plants. Besides this, SiNPs150 mg kg−1 elevated antioxidant enzymes activities which scavenging ROS and reduced Cr-caused oxidative destruction. Furthermore, qPCR assay showed upregulation of the antioxidant defense related genes with the application of SiNPs under Cr stress. Transmission Electron Microscopy analysis showed that SiNPs application effectively alleviated Cr-induced damage to leaf ultrastructure and had a substantial impact on Cr and Si accumulation in plants. In conclusion, the utilization of green SiNPs as nano-fertilizers exhibits great potential as a strategy for agriculture to alleviate the adverse effects of HMs stress, safeguard food safety, and sustainable agriculture in the future.