Silica nanoparticles (SiO2 NPs) have numerous applications in agriculture, but may also pose significant risks to plants. Nevertheless, their bioaccumulation, an important determinant of their risks, was often not accurately measured due to the lack of reliable methods. In this study, the accumulation in rice seedlings of SiO2 NPs of different sizes without and with a gold nanoparticle core (Au@SiO2 NPs) was examined. Potential interference from SiO2 NP dissolution was minimized by lowering the pH of the uptake medium, which did not result in any observable adverse bioeffects. Under this condition, the direct determination of Si showed the significant accumulation of SiO2 NPs in roots and shoots and a decrease in the accumulation of SiO2 NPs in shoots with increasing particle size. However, when accumulation was monitored using Au@SiO2 NPs, SiO2 NP accumulation was significantly higher when measured by direct Si determination than by Au determination, indicating that the former overestimates the accumulation of SiO2 NPs. Consequently, unlike direct Si determination, tracking the gold nanoparticle core revealed an increase in SiO2 NP accumulation in shoots with increasing particle size. Overall, accurate determination of SiO2 NP bioaccumulation is imperative for appropriate bioapplications and reliable biosafety assessments of these particles.