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Chlorothalonil (2,4,5,6-tetrachloro-1,3-benzenedicarbonitrile, TPN, CAS: 1897-45-6) is a halogenated fungicide currently widely applied to a large variety of crops. Its carcinogenicity, embryo lethality, and high chronic oral toxicity in mammals, among other effects on a variety of organisms, has made its biodegradation of great interest. Chlorothalonil dehalogenase (Chd) from the bacterium Pseudomonas sp. CTN-3 offers a potential solution by catalyzing the first step in the degradation of chlorothalonil. Reported herein are active biomaterials of Chd when encapsulated in tetramethylorthosilicate (TMOS) gels using the sol–gel method (Chd/sol), alginate beads (Chd/alginate), and chitosan-coated alginate beads (Chd/chitosan). Both Chd/sol and Chd/chitosan increased protection from the endopeptidase trypsin as well as imparted stability over a pH range from 5 to 9. Chd/sol outperformed Chd/alginate and Chd/chitosan in long-term storage and reuse experiments, retaining similar activity to soluble Chd stored under similar conditions. All three materials showed a level of increased thermostability, with Chd/sol retaining >60% activity up to 70 °C. All materials showed activity in 40% methanol, suggesting the possibility for organic solvents to improve TPN solubility. Overall, Chd/sol offers the best potential for bioremediation of TPN using Chd.