The main focus of this review is recent advances in the preparation of bio-based nanostructures. The structures especially prepared from natural resources have recently gained an interest in researchers’ work. We summarize novel routes of application in medicine as drug delivery systems and in environmental protection. Additionally, their important practical utility in 3D and 4D printing, microfluids-based synthesis or lab-on-a-chip and organ-on-a-chip has been emphasized. Finally, we discuss possible future developments and challenges, which may in the future have and influence on industrial and scientific processes. Nanostructures can be presented in various shapes, including spheres, boxes, tubes, nanorods and nanohorns. A variety of different shapes are discussed. A significant part of this review is focused on spherical structures, which have gained great popularity because of their unique properties and unlimited potential for applications. In most cases they are prepared using inorganic, organic compounds or hybrid materials. Recently there has been increasing interest in the fabrication of bio-based nanostructures. Natural polymers, including lignin, chitin, cellulose, starch, as well as peptides (e.g. collagen or zein) can serve as substrates for the production of such particles. These materials are often plant derivatives or by-products of industrial processes, and are cheap and environmentally friendly. Being nontoxic and biocompatible, they offer possible uses in contrast imaging, as sensors, and as selfcleaning and anticorrosion surfaces. More of the potential application routes are also described.