Controlled-release fertilizers (CRF) are needed under current agriculture practice to decrease the environmental impact caused by fertilizer doses applied in excess of plants’ uptake rate. Commercial CRF are available. They are manufactured from mineral fertilizers encapsulated into a synthetic polymer matrix or coated by a polymer layer. However, substitution of fossil sourced organic polymers with biopolymers is a major environmental concern. In the present paper, we describe the manufacture by a continuous twin-screw extrusion process, and the mechanical and chemical properties of injection-molded composite pellets containing 90% sunflower protein concentrate (SPC) matrix, and 5–10% of a biopolymer (BP) obtained from municipal biowastes (MBW), and/or urea (U). The reported results show that SPC-BP-U behaves as an efficient eco-friendly CRF. BP contributes to several benefits to the performance of the composite pellets, upon increasing surface hardness, and controlling the formation of ammonia from urea hydrolysis and the release of organic nitrogen. The SPC-BP-U appears a powerful eco-friendly CRF to supply organic C and the three major N, P, and K nutrients to soil and plants. It offers worthwhile scope for being tested in the cultivation of specific plants under the real operational conditions of agriculture practices.