Biomass from grasses such as sugarcane contains bodies of biogenic silica, the phytoliths. In industrial biomass processing, phytoliths can be harmful to equipment causing wear and ash deposits. However, phytoliths can also be beneficial if they are valorized into silica-based products. This work investigates the fate of phytolith in the industrial crushing of sugarcane stalks using biomass fractionation, ashing, and imaging techniques. Phytoliths can be traced by scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy (SEM-EDS) due to their proximity to the outer surface and fingerprint size, shape, and chemistry. In native sugarcane stalks, phytoliths are concentrated in the epidermal region. Industrial crushing promotes tissue ruptures that transform stalks into bagasse, where the epidermal tissues and phytoliths are found with preserved integrity, fractured, or even detached from the native tissue structures. The observations presented in this work suggest novel strategies for the isolation of phytoliths in biorefinery designs integrable to the well-established industrial crushing of sugarcane stalks.