Background: A microgranule fertilizer was designed for localized fertilization of soil with controlled release of nutrients. The microgranule matrix was fortified with proteins, which were obtained from food industry byproducts or waste, i.e., whey protein from milk serum, soy protein from soy isolate and egg white protein from chicken egg white powder. The mechanism of the protein decomposition and migration of micro and macromolecule compounds through two different model soil systems was investigated. The potential of the protein fortified fertilizer for localized fertilization of the potted maize seeds was evaluated. Results: The study revealed that proteins slowly diffused through soil with simultaneous degradation, which was accompanied with release of ammonia ions. The highest concentration of proteins and degradation products was found in a close vicinity of the microgranule. The microgranules were used as a local fertilizer for maize seeds in the pot experiments. The experiments confirmed statistically significant improvement in root density of maize plant compared to control group. Conclusions: Byproducts or waste of food industry, such as the milk serum and soy can be used as a source of proteins that degrade in soil without a pretreatment. The degradation is accompanied with formation of ammonium ions, which can be utilized by plants as a nitrogen source. The fertilizer microgranule should be placed in a close vicinity to the plant seed, since the maximum of the protein concentration and ammonia ions is reached at a very close distance from the microgranule.