Amorphous silica formed by thermally oxidizing silicon is commonly eligible for lithographic patterning or can be grown on patterned substrates. However, it is still a challenge to combine controlled microstructuring with controlled crystallization of SiO2. Here, it is shown that traces of volatile lithium species transported through the gas phase catalyze the crystallization of silica integrated into common silicon microstructures. The selected crystallization temperature determines which polymorph forms. As an example, the formation of quartz, tridymite, and cristobalite microtubes by thermally oxidizing macroporous silicon is investigated. Lithium-induced crystallization may extend state-of-the-art silicon technology and yield nano- and microstructures consisting of different silica polymorphs, which are, in contrast to many functional oxides, nontoxic.