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Biofumigation was proposed as an alternative to synthetic pesticides for the disinfection of agricultural soils, in view of the biocidal effect of isothiocyanates (ITCs) released by some vegetal species, like Brassicaceae. However, biofumigation also presents limitations; thus, a novel and viable alternative could be the direct introduction of ITCs into agricultural soils as components loaded into biodegradable hydrogels. Thus, in this work, ITCs-based microemulsions were developed, which can be loaded into porous polymer-based hydrogel beads based on sodium alginate (ALG) or sodium carboxymethyl cellulose (CMC). Three ITCs (ethyl, phenyl, and allyl isothiocyanate) and three different surfactants (sodium dodecylsulfate, Brij 35, and Tween 80) were considered. The optimal system was characterized with attenuated ATR-FTIR spectroscopy and differential scanning calorimetry to study how the microemulsion/gels interaction affects the gel properties, such as the equilibrium water content or free water index. Finally, loading and release profiles were studied by means of UV–Vis spectrophotometry. It was found that CMC hydrogel beads showed a slightly more efficient profile of micelles’ release in water with respect to ALG beads. For this reason, and due to the enhanced contribution of Fe(III) to their biocidal properties, CMC-based hydrogels are the most promising in view of the application on real agricultural soils.