An innovative approach for the production of bio-micro/nanostructures with high-value compounds from agricultural by-products was studied. This research aimed to valorize bioactive compounds existing in the by-products of the plants of Fragaria vesca (wild strawberry). The particle characteristics, morphology, size, release properties, and antioxidant activity of micro/nanostructures containing the extract of by-products of the plants of Fragaria vesca or quercetin (one of the main polyphenols in the plant) were analyzed. The electrohydrodynamic (EHD) technique was utilized for encapsulation. The results showed that the morphology and size of the structures were influenced by the concentration of zein, with 10% w/v zein concentration leading to irregular and non-uniform nanostructures, while 20% w/v zein concentration resulted in a mixture of microparticles and thin fibers with an irregular surface. The type and concentration of the core material did not significantly affect the morphology of the micro/nanostructures. In vitro release studies demonstrated the controlled release of the core materials from the zein micro/nanostructures. The release profiles were analyzed using the Korsmeyer–Peppas and Weibull models, which provided insights into the release mechanisms and kinetics. The most relevant release mechanism is associated with “Fickian Diffusion”. The antioxidant activity of the structures was evaluated using an ABTS radical-scavenging assay, indicating their potential as antioxidants. In conclusion, the EHD technique enabled the successful encapsulation of Fragaria vesca by-product extract and quercetin with zein, resulting in micro/nanostructures with different morphologies.