The study aims at reusing and recycling the protein hide waste from the leather industry in ecological conditions by elaborating an innovative procedure in order to obtain a collagen matrix functionalized with nitrogen, phosphorus, and potassium (NPK) nutrients to be used for preparing smart fertilizers. This is an interdisciplinary approach, as it starts from hide waste raw material as a critical industrial waste, which is then subjected to several technological steps by selection of optimal processing parameters, followed by product fabrication at the laboratory, and next scales to the industrial pilot plant to obtain novel agro-hydrogels. In this context, the technology scheme for collagen hydrolysate with encapsulated nutrients was proposed and the process parameters were optimized by functionalization of agro-hydrogels with various natural and synthetic polymers, such as polyacrylamide, poly(sodium 4-styrenesulfonate-co-glycidyl methacrylate) copolymer, starch or dolomite. Based on the laboratory experiments, a pilot plant was constructed and tested. Taking as reference the collagen hydrolysate with encapsulated nutrients, the new fertilizers were adequately characterized by chemical analysis, determination of biodegradability and the degree of release of oxidable compounds in water. Based on the biodegradation mechanism and kinetic analysis of oxidable compounds release, adequate arguments are evidenced to demonstrate that these fertilizers can be applied for amendment of poor agricultural soils.