Crystalline silica (SiO2) is recurrently identified at the percent level in the infrared spectra of protoplanetary disks. By contrast, reports of crystalline silica in primitive meteorites are very unusual. This dichotomy illustrates the typical gap existing between astrophysical observations and meteoritical records of the first solids formed around young stars. The cometary samples returned by the Stardust mission in 2006 offer an opportunity to have a closer look at a silicate dust that experienced a very limited reprocessing since the accretion of the dust. Here, we provide the first extended study of silica materials in a large range of Stardust samples. We show that cristobalite is the dominant form. It was detected in 5 out of 25 samples. Crystalline silica is thus a common minor phase in Stardust samples. Furthermore, olivine is generally associated with this cristobalite, which put constraints on possible formation mechanisms. A low-temperature subsolidus solid–solid transformation of an amorphous precursor is most likely. This crystallization route favors the formation of olivine (at the expense of pyroxenes), and crystalline silica is the natural byproduct of this transformation. Conversely, direct condensation and partial melting are not expected to produce the observed mineral assemblages. Silica is preserved in cometary materials because they were less affected by thermal and aqueous alterations than their chondritic counterparts. The common occurrence of crystalline silica therefore makes the cometary material an important bridge between the IR-based mineralogy of distant protoplanetary disks and the mineralogy of the early solar system.