Flaxseed proteins exhibit functionalities interesting for the food industry, including antioxidant capacity. Antioxidant activity depends on the protein composition and the presence of phenolic compounds extracted with them from the matrix. The research focused on the effect of subsequent protein extractions (water, salt and alkaline) of flaxseed meals (of three cultivars) on the protein fraction composition and its relations to antioxidant capacity. The protein and phenolic profiles and antioxidant functionalities (in antiradical ORAC and emulsion assays) were analysed. Spectroscopic characteristics of the fractions (fluorometric and FT-IR analysis) were also included. Our study has shown the effect of fractionation on the share of proteins at MW from 56–38 kDa (globulin-like) and <15 kDa (albumin-like) in the protein profiles. The highest globulin share was in the alkaline-extracted fractions (AEF) and albumin in the salt-extracted (SEF) ones. SDG (secoisolariciresinol diglucosides) and phenolic acids (p-coumaric and ferulic) were extracted with flaxseed proteins. Their contents were fraction-dependent and the highest in AEF. The concentration of phenolics in AEF corresponded with the highest antiradical capacity (ORAC) compared with the other fractions. However, the SEF showed a higher ability to inhibit oxidation in emulsions than AEF, which could be associated with the higher content of the low MW proteins.