The UN 2030 Agenda for Sustainable Development established the goal of cutting the use of pesticides in the EU by 50% by 2030. However, a ban on pesticides could seriously affect the productivity of agriculture, resulting in severe issues due to global hunger and food deficiency. Controlled release (CR) of bioactive chemicals could play a valid alternative in this context. To this aim, two biodegradable polymers, namely sodium alginate (AL) and sodium carboxymethylcellulose (CMC), were employed to obtain crosslinked hydrogel beads for the encapsulation and CR of glycoalkaloids extracted from tomato and potato leaves to be used as biocompatible disinfectants for agricultural soils. The physico-chemical characterization of the controlled-release systems was carried out by means of Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy, Scanning Electron Microscopy (SEM), thermogravimetry (TGA), differential scanning calorimetry (DSC) (FWI > 80%) and drying kinetics. The plant extracts and the encapsulation efficiency (~84%) were, respectively, characterized and evaluated by High-performance Liquid Chromatography-Mass Spectrometry (HPLC-MS). Finally, preliminary microbiological tests were conducted to test the efficacy of the most promising systems as biocidal formulations both in the lab and on a model soil, and interesting results were obtained in the reduction of bacterial and fungal load, which could lead to sustainable perspectives in the field.