This work aims at assessing the crystallization process of amorphous silica from rice husk (RH) by in situ X-ray diffraction, upon heating up to 1450 °C in a high-temperature chamber. The study includes microstructural characterization by transmission electron microscopy. The work was conducted on rice husk ash (RHA), obtained by combustion of RH at 650 °C with and without leaching in 1 N HCl solution, obtaining samples with variable impurity content. The results showed that crystallization of RHA amorphous silica upon continuous heating occurred at higher temperatures compared to the isothermal one, considering the sample purity. The type of polymorph silica identified in the samples during continuous heating consisted of cristobalite or a combination of cristobalite and tridymite depending on the impurity levels in the samples. The study revealed silica crystallites with spherical shape nucleated by a dominant homogeneous mechanism. The size of crystallites ranges from around 2 nm to 20 nm. Larger particles nucleated on impurities and constituted by combinations of P, Ca, K, Mg, and Na were also observed.