This work addresses environmental problems connected with biowaste management, the chemical industry, and agriculture. These sectors of human activity cause greenhouse gas (GHG) emissions in the air, climate change, leaching of excess mineral fertilizers applied to soil into ground water, and eutrophication. To mitigate this problem in agriculture, controlled release fertilizers (CRFs) are made by coating mineral fertilizers granules with synthetic polymers produced from the fossil-based chemical industry. This strategy aggravates GHG emission. In the present work, six formulations containing sunflower protein concentrate (SPC) and a new biopolymer (BP) obtained from sunflower oil cake and by hydrolysis of municipal biowaste, respectively, and commercial urea were tested as CRFs for spinach cultivation against the control growing substrate Evergreen TS and commercial Osmocote®. The results show large differences in plants’ nitrate concentration due to the different treatments, although the same nitrogen amount is added to the substrate in all trials. BP is the key component mitigating nitrate accumulation in plants. The plants grown in the substrates containing BP together with SPC and/or urea, although exhibiting relatively high total N uptake (47–52 g kg−1), have significantly lower nitric to total N ratio (9.6–12.0) than that (15.3–16.5) shown by the plants grown in the substrates containing SPC and/or urea, but no BP. The data confirm that all composites containing BP yield the safest crop coupled with high biomass production. Replication of BP effects for the cultivation of different plants will contribute to the development of a biobased chemical industry exploiting biowastes as feedstock.