With their excellent biocompatibility, adjustable size, and high specific surface area, silica nanoparticles (SiO2 NPs) offer an alternative to traditional bulk fertilizers as a means to promote sustainable agriculture. SiO2 NPs have been shown to promote the growth of plants and to reduce the negative effects of biotic and abiotic stresses, but their bioaccumulation is a crucial factor that has been overlooked in studies of their biological effects. In this review, the techniques to quantify and visualize SiO2 NPs in plants were examined first. We then provide a summary of the current state of knowledge on the accumulation, translocation, and transformation of SiO2 NPs in plants and of the factors (e.g., the physicochemical properties of SiO2 NPs, plant species, application mode, and environmental conditions) that influence SiO2 NP bioaccumulation. The challenges in analyzing NP-plant interactions are considered as well. We conclude by identifying areas for further research that will advance our understanding of NP-plant interactions and thus contribute to more sustainable, eco-friendly, nano-enabled approaches to improving crop nutrient supplies. The information presented herein is important to improve the delivery efficiency of SiO2 NPs for precision and sustainable agriculture and to assess the safety of SiO2 NPs during their application in agriculture.