Each year a large amount of agro-industrial by-products are generated as a result of the processing of agricultural materials. These products have been generally used as animal feeds. However, they are rich in fiber, protein, minerals, especially bioactive components such as fatty acid, phenolic components, antioxidant and antimicrobial substances. Numerous scientific researches have been reported regarding the production of antimicrobial and antioxidant products from agro-industrial by-products such as rice bran, wheat germ, rice husk, vegetable peels, fruit seeds, and essential oils from the peel and seeds of various plants. Nowadays, novel strategies have been developed to evaluate by-products generated annually by agro-industrial processing. Nanotechnology is one of the most promising methods to evaluate the bioactive components of by-products. Nanotechnology offers many advantages compared to conventional methods. Nanoscale materials enable an expanded surface area providing more contact areas with food. Also, nanotechnology offers solutions to technological challenges by creating systems that are more resistant to external and internal factors such as heat, light, oxygen, enzymes, etc. This chapter focuses on the antimicrobial, antioxidant properties of cereal/grain, fruit, and vegetable by-products, and the productions and application of different bioactive components obtained from agro-industrial by-products with nanotechnological methods. Two different perspectives are evaluated in the chapter. Firstly; the importance, antioxidant, antimicrobial properties, and the utilization of by-products in different food systems are given, secondly; formulation, the potential usage, and the applications of bioactive nanomaterials obtained from agro-industrial by-products are presented.