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The metabolic actions of storage fungi and other microorganisms can cause spoilage and post-harvest losses in agricultural commodities, including flaxseed. These microbial contaminants are oxidized with hydroxyl radicals that are efficiently generated when ozone, hydrogen peroxide (H 2 O 2 ) and ultraviolet (UV) light react in an advanced oxidative process (AOP). The present work explores what we believe is the first application of an AOP technology to reduce mould on whole brown and yellow flaxseed. The impact of AOP on storage and quality parameters was assessed by measuring the fatty acid value (FAV), germination rate, moisture content (MC) and visible mould growth after 12 weeks of storage at 30°C and 75% relative humidity (RH). Under these conditions, the yellow decontaminated flaxseed showed a 31% decrease in the number of seeds with visible mould without any adverse effect on germination rate, FAV and MC. In contrast, the same AOP treatment created an insignificant decrease in mould in stored brown flaxseed, at the cost of decreasing the germination rate and increasing FAV. The adverse effects of AOP on brown flaxseed were not readily apparent but became measurable after storage. Moreover, Fourier transform infrared (FTIR) spectroscopy was utilized to explore the rationale behind the different reactions of flaxseed varieties to AOP. The corresponding results indicated that the tolerance of yellow flaxseed to AOP might be related to its richness in olefins. The authors believe that technologies that harness advanced oxidative processes open new horizons in decontamination beyond ozone alone and towards increasing the shelf life of various agri-food products., Competing Interests: Conflict of InterestThe authors declare no competing interests., (© The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2023, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)