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BACKGROUND: The relatively inferior techno‐functionality of flaxseed protein/polysaccharide complexes, especially regarding emulsifying and antioxidant activities, has partially limited their implication in the health food system. The present study aimed to investigate the effects of an atmospheric pressure plasma jet (APPJ) on the physicochemical, structural and selected techno‐functional properties of flaxseed extracts. RESULTS: The results obtained showed that the full‐fat and defatted flaxseed extract solutions (5 mg mL–1) displayed a sustainable decline in pH (−54.06%, −48.80%, P < 0.05) and zeta potential values (−29.42%, −44.28%, P < 0.05), but a gradual increase in particle sizes, as visualised by an optical microscope, during 0–120 s of APPJ treatment. Moreover, the APPJ led to initial decrease but subsequent increase in protein carbonyls and secondary lipid oxidation products, and concurrently changed the spatial conformation and microstructure of flaxseed extracts, as indicated by endogenous fluorescence properties and scanning electron microscopy (SEM). Additionally, the protein subunit remodeling and gum polysaccharides depolymerization were different for full‐fat and defatted flaxseed extracts after 30 s of APPJ exposure. Importantly, the emulsifying and antioxidant activities of defatted flaxseed extract were particularly improved, as assessed by cyro‐SEM and 2,2‐diphenyl‐1‐picrylhydrazyl radical scavenging activity following 15–30 s of APPJ treatment, as a result of the changing interactions between protein and gum polysaccharides, as well as the release of specific phenolic compounds. CONCLUSION: APPJ could serve as a promising strategy for tailoring the specific techno‐functionality of flaxseed extracts based on mild structural modification. © 2021 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]