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Novel bio-based nanocomposites were developed as carriers for loading and sustained-release of vanillin (Van.) and cinnamaldehyde (Cinn.) antioxidants. The composites were obtained by intercalation of chitosan (CS) into sodium montmorillonite (CS/Mt), incorporation of chitosan with polyaniline (CS/PANI) and chitosan/polyaniline/exfoliated montmorillonite (CS/PANI/Mt). The structure and morphology of composites were characterized by FTIR, XRD, SEM and TEM. The release data of Van. and Cinn. from CS and CS/Mt obeyed well zero-order equation. However, Higuchi and Korsmeyer-Peppas models fitted well the release data from CS/PANI and CS/Mt composites. Their antifungal activity was examined towards Fusarium oxysporum and Pythium debaryanum. In vitro assay, CS, Cinn., Van., CS/PANI and CS/PANI/Cinn., have a strong inhibitory effect on the linear growth of the target pathogens, even at lower concentrations. Greenhouse assay indicated that seedling treatment by the loaded CS/PANI/Cinn and CS/Mt/Cinn. reduced both disease index and disease incidence parameters of both pathogens and possessed seedlings growth promoting potential of tomato compared to untreated-infected controls.