Silicon nanoparticles (SiNPs) have been widely used to immobilize toxic trace metal(loid)s (TTMs) in contaminated croplands. However, the effect and mechanisms of SiNP application on TTM transportation in response to phytolith formation and phytolith-encapsulated-TTM (PhytTTM) production in plants are unclear. This study demonstrates the promotion effect of SiNP amendment on phytolith development and explores the associated mechanisms of TTM encapsulation in wheat phytoliths grown on multi-TTM contaminated soil. The bioconcentration factors between organic tissues and phytoliths of As and Cr (> 1) were significantly higher than those of Cd, Pb, Zn and Cu, and about 10 % and 40 % of the total As and Cr that bioaccumulated in wheat organic tissues were encapsulated into the corresponding phytoliths under high-level SiNP treatment. These observations demonstrate that the potential interaction of plant silica with TTMs is highly variable among elements, with As and Cr being the two most strongly concentrated TTMs in the phytoliths of wheat treated with SiNPs. The qualitative and semi-quantitative analyses of the phytoliths extracted from wheat tissues suggest that the high pore space and surface area (≈ 200 m2 g−1) of phytolith particles could have contributed to the embedding of TTMs during silica gel polymerization and concentration to form PhytTTMs. The abundant Si–O functional groups and high silicate-minerals in phytoliths are dominant chemical mechanisms for the preferential encapsulation of TTMs (i.e., As and Cr) by wheat phytoliths. Notably, the organic carbon and bioavailable Si of soils and the translocation of minerals from soil to plant aerial parts can impact TTM sequestration by phytoliths. Thus, this study has implications for the distribution or detoxification of TTMs in plants via preferential PhytTTM production and biogeochemical cycling of PhytTTMs in contaminated cropland following exogenous Si supplementation.