Polyethylene terephthalate (PET) is one of the most produced plastic materials in the world. The emergence of microplastics and nanoplastics (MPs/NPs) as a significant environmental contaminant has become a matter of increasing concern. While the toxicological effects of PET NPs have been widely researched, there is a lack of methodologies for studying their accumulation. The present study introduces a novel method to monitor the distribution of PET NPs in germinating wheat (Triticum aestivum L.) seeds. This involves the functionalization of superparamagnetic iron oxide nanoparticles (SPIONs) with PET NPs (PET–fSPIONs) coupled with magnetic resonance microimaging (µMRI) to provide insight into their distribution within the seed. The present study has demonstrated that PET–fSPIONs accumulate in specific regions of germinating wheat seeds, including the shoot apical meristem, the radicle, the coleoptile, the plumule, and the scutellum. Furthermore, the accumulation of PET–fSPIONs has been shown to exert a discernible effect on spin–spin relaxation (T2), as observed via MRI and quantitative T2 relaxation time analysis. The accumulation of PET NPs in embryo regions was also confirmed by SEM. Diffusion-weighted magnetic resonance imaging (DW-MRI) and non-invasive chemical shift imaging analyses demonstrated that PET NPs resulted in restricted diffusion within the highlighted areas, as well as an impact on lipid content. Our study reveals that using µMRI with fSPIONs provides a non-invasive method to monitor the biodistribution of PET nanoparticles in wheat seeds. Additionally, it offers valuable insights into the microstructural interactions of PET.