Barley is one of the most consumed cereals, with many different cultivars available worldwide. Like other crops, its yield has been affected by climate change and soil degradation. This work proposes controlled-release protein-based matrices with incorporated zinc to improve barley seed germination and zinc content in the plant. Thus, the main objective of this study was to investigate the use of controlled-release protein-based matrices for massive crops, such as barley. Different barley cultivars of barley were studied: Barke, Golden Promise, Morex, WB-200, WB379, and WB-446. The seeds of each cultivar were also analyzed in order to explain the behavior of plants observed during the growth. To this end, the physico-chemical (FT-IR, Raman spectroscopy, and Zn concentration) and microstructural (SEM) properties of the different seeds were firstly evaluated to establish differences between the studied cultivars. In addition, the use of controlled-release soybean protein-based matrices without zinc (M) or with zinc incorporated (MZ) was evaluated as fertilizers in the different barley cultivars. In this sense, the use of these matrices as a zinc carrier improved seed germination and zinc content in the plants, indicating that the use of matrices improves the amount of zinc assimilated by the crops (up to 30 and 50% with M and MZ, respectively) and allows the proper root growth of all cultivars of barley. In conclusion, this article shows the potential of controlled-release protein-based matrices as substitutes for conventional fertilization.