Formation of microcrystalline quartz formation has proven to be effective at preserving porosity in deeply buried sandstone petroleum reservoirs, typically cemented by syntaxial quartz cement. There remains much uncertainty about what controls the growth of microcrystalline quartz and how it prevents syntaxial quartz overgrowths. Here, the Cretaceous Heidelberg Formation, Germany, provides a natural laboratory to study silica polymorphs and develop an understanding of their crystallography, paragenetic relationships, and growth mechanisms, leading to a new understanding of the growth mechanisms of porosity-preserving microcrystalline quartz. Data from scanning electron microscopy (SEM), electron backscatter diffraction (EBSD), and transmission electron microscopy (TEM) data illustrate that porosity-preserving microcrystalline quartz cement is misoriented with respect to the host grain upon which it grows. In contrast, ordinary quartz cement grows in the same orientation (epitaxially) as the host quartz sand grain, and typically fills pore spaces. EBSD and TEM observations reveal nanofilms of amorphous silica (∼ 50–100 nm in thickness) between the microcrystalline quartz and the host grain. The microcrystalline quartz is interpreted to be misoriented relative to the host grain, because the amorphous silica nanofilm prevents growth of epitaxial quartz cement. Instead, the microcrystalline quartz is similar to chalcedony with [11–20] perpendicular to the growth surface and c axes parallel with, but randomly distributed (rotated) on, the host quartz grain surface. Development of pore-filling quartz growing into the pore (in the fast-growing c-axis direction) is thus inhibited due to the amorphous silica nanofilm initially and, subsequently, the misoriented microcrystalline quartz that grew on the amorphous silica.