Application of iron (Fe)- and silica (Si)-enhanced biochar compound fertilisers (BCF) stimulates rice yield by increasing plant uptake of mineral nutrients. With alterations of the nutrient status in roots, element homeostasis (e.g., Fe) in the biochar-treated rice root was related to the formation of biominerals on the plaque layer and in the cortex of roots. However, the in situ characteristics of formed biominerals at the micron and sub-micron scale remain unknown. In this study, rice seedlings (Oryza sativa L.) were grown in paddy soil treated with BCF and conventional fertilizer, respectively, for 30��days. The biochar-induced changes in nutrient accumulation in roots, and the elemental composition, distribution and speciation of the biomineral composites formed in the biochar-treated roots at the micron and sub-micron scale, were investigated by a range of techniques. Results of laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) showed that biochar treatment significantly increased concentrations of nutrients (e.g., Fe, Si, and P) inside the root. Raman mapping and vibrating sample magnetometry identified biochar particles and magnetic Fe nanoparticles associated with the roots. With Fe plaque formation, higher concentrations of FeOx��� and FeOxH��� anions on the root surface than the interior were detected by time-of-flight secondary ionization mass spectrometry (ToF-SIMS). Analysis of data from scanning electron microscopy energy-dispersive spectroscopy (SEM-EDS), and from scanning transmission electron microscopy (STEM) coupled with EDS or energy electron loss spectroscopy (EELS), determined that Fe(III) oxide nanoparticles were accumulated in the crystalline fraction of the plaque and were co-localized with Si and P on the root surface. Iron-rich nanoparticles (Fe���Si nanocomposites with mixed oxidation states of Fe and ferritin) in the root cortex were identified by using aberration-corrected STEM and in situ EELS analysis, confirming the biomineralization and storage of Fe in the rice root. The findings from this study highlight that the deposition of Fe-rich nanocomposites occurs with contrasting chemical speciation in the Fe plaque and cortex of the rice root. This provides an improved understanding of the element homeostasis in rice with biochar-mineral fertilization.