Linseeds contains high levels of PUFA α-linolenic acid, naturally protected against thermal oxidation by their encapsulation within LS oil bodies by multiple components including antioxidant proteins and mucilage emulsifying agents. By LS grinding, adding of water, adjusting pH, and sonication LS oil bodies emulsions (LSE) can be formed which can also encapsulate externally added PUFAs, to minimize their thermal oxidation, as it does for the intrinsic ALA PUFAs. Fish oil encapsulation into this LSE platform (LSFE) offers the possibility of a nutritive delivery system of the biologically essential PUFA fish oil’s, protected from oxidation, which to date is difficult to achieve. In this study structural and chemical properties LF 1H NMR T1-T2 characterization of LSE and LSFE was used to analyze their stability and changes, under thermal oxidizing conditions. Peak changes in these LF 1H-NMR spectra were correlated with the stability of chemical and physical variables during thermal (55oC for 96 hrs) oxidation. The present study demonstrates the capability of 1H LF-NMR relaxation sensor to monitor the time domain fingerprints of chemical and structural changes of LSE and with co-encapsulated fish oil (LSFE) under thermal autoxidation conditions. The results of the LF-1H NMR analysis are further supported and correlated with conventional peroxide value tests, self-diffusion, droplets size distribution, zeta potential estimation of surface stability under thermal oxidation conditions. The results of this study demonstrate the efficacy of LSE to minimize linseed and encapsulated fish oil PUFA oxidation.