Flaxseed (Linum usitatissimum L.) protein is reported to release physiologically important amino acids and bioactive peptides during gastrointestinal (GI) digestion. The effect of seed mucilage and oil and thermal processing on the in vitro protein digestibility (IPD) of flaxseed protein was assessed under simulated GI digestion. Protein in ground whole flaxseed that contained both mucilage and oil had the lowest digestibility (12.61%). Baking and boiling before size reduction significantly (P < 0.05) improved the IPD (31.77% and 28.04%, respectively). Further increase in IPD occurred when mucilage (51.00%) and both mucilage and oil (66.79%) were removed. Isolated flax protein had a similar IPD value (68.00%) as the mucilage and oil–removed flaxseed. The polypeptide of approximately 13 kDa showed resistance to GI digestion compared with other polypeptides of all these treated seeds. Removal of oil and mucilage as well as thermal treatment enhanced protein digestibility of flaxseed.