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Rapeseed oilcake or press-cake is generated as bulk waste during oil extraction from oilseeds. Owing to its high protein content, further processing of oilcakes into vegetable protein generates large quantities of fibrous residue (“oil-and-protein” spent meal) as by-product, which currently has very limited practical utility. Here, we report hydrothermal carbonization of this industrial waste to convert it into carbon nanoparticles, bestowed with multitude of functionalities. We demonstrate that these nanoparticles can be assembled into micrometer-sized spheres when precipitated from water by acetone. These microspheres, with their added feature of hemocompatibility, can be potentially utilized as an encapsulation vehicle for the protection of thermolabile compounds (such as protein); however, the secondary and tertiary features of the protein were marginally perturbed by the encapsulation process. The synthesized carbon nanoparticle was found to be an effective biocidal agent, exhibiting bacterial cellular damage and complex formation with the bacterial plasmid (evident from ethidium bromide exclusion assay), which are critical for cell survival. The results show the ability to convert industrial biowaste into useful nanomaterials for use in food industries and also suggest new scalable and simple approaches to improve environmental sustainability in industrial processes.