Phase transformation and optical properties of silica (silicon dioxide, SiO2) quartz sand under high pressure/temperature has been of interest in geology and optical physics for many years. In this study, besides high pressure/temperature, high plastic strain is simultaneously applied to the quartz sand by high-pressure torsion (HPT) processing. The material shows oxygen vacancy formation and transformation to (a) a denser nanocrystalline quartz phase, (b) a high-temperature amorphous phase and (c) a high-pressure coesite phase. These structural and microstructural changes lead to light absorbance, electron spin resonance, photoluminscence and photocatalytic activity, while these changes are enhanced by increasing strain. This study introduces a possible pressure-temperature-strain-based mechanism for the formation of naturally observed vacancies and coesite phase in SiO2-based minerals and sands.