Phytochemicals are chemical compounds produced by plants that play key roles in their growth and defense and have also been actively involved in corrosion inhibition of metals and alloys. The action of these phytochemicals as inhibitor molecules in an aggressive environment is triggered by the presence of heteroatoms and other adsorption sites capable of chelating with the metal ions forming complexes that provide a protective film for the metal. This protective film blocks the active sites on the metal from further interaction with the aggressive environment. The efficiency of corrosion inhibitors in coating formulations requires the compounds to be safely encapsulated prior to when triggered. This prevents leaching and early interactions with the coating matrix and is a preferred carrier mode than when directly spiked in the coating matrix. The flavonoid Quercetin (QCT) present in a wide variety of plants was explored. QCT contains five electroactive hydroxyl groups in addition to the carboxylic, carbonyl, and aromatic groups which provides three potential coordination sites for interaction with the metal ions. When loaded in silica nanocontainers, the phytochemical was evaluated for active corrosion protection of aluminium alloy 6061 in the prepared self-healing coatings. The corrosion protection offered by QCT was investigated with electrochemical impedance spectroscopy in an aggressive chloride environment. Chemical transformation experienced by QCT was influenced by pH and a protective film was detected in the defective zone of the examined coupons.