Silica nanoparticles (SiNPs) are one of the most promising nanoparticles in stimulating plant growth and alleviating environmental stresses. Besides beneficial attributes, these nanoparticles may also possess serious toxicity issues. In this context, the present study aimed to evaluate the dose and size-dependent toxicity attributes of SiNPs using Allium cepa root tip assay. The dose-dependent study conducted using moderate-size SiNPs (∼50 nm) with different concentrations (1-500 g/L) depicted non-toxic effects up to the dose of 75 g/L. However, concentrations above 100 g/L imparted a gradual increase in toxicity with the increasing dosage of SiNPs, where mitotic index (MI) was reduced, and chromosomal aberration (CA), ROS accumulation, and membrane disruption increased significantly. Moreover, among the 3 different sizes of SiNPs viz. ∼30, ∼50, and ∼100 nm, ∼50 nm was relatively non-toxic. Further, a significant reduction in toxicity level at higher concentrations (≥200 g/L) was achieved when the SiNPs (∼50 nm) surface was functionalized with glucose (GSiNPs) and trehalose (TSiNPs) compared to bare SiNPs. In this context, the reduction in CA by GSiNPs was 1.6-2.9 folds and by TSiNPs 1.9-3.3 folds. Also, GSiNPs and TSiNPs improved the plant growth and soil microflora colonization, without imparting toxic effects.