Dietary flaxseed is being studied as an alternative or complementary therapy to medications for reducing risk factors related to cardiovascular disease progression. The suggested benefits of alpha-linolenic acid (ALA) as an antihypertensive agent, of secoisolariciresinol diglucoside (SDG) derived enterolignans as antioxidants and estradiol mimetics and dietary fiber for its role in cholesterol lowering are just some of the potential benefits of consuming flaxseed. These studies have progressed from dietary studies involving animal models to large-scale clinical trials with the ultimate goal of adopting its consumption by the general public. To promote adherence in long-term clinical trials and encourage its consumption by the general public, flaxseed in one of its various forms or as its isolated bioactive ingredients is either incorporated into food products, called functional foods, or sprinkled onto foods before consumption. The stability of these bioactives in any of these forms becomes crucial for its acceptance by these populations and in order to optimize its biological actions. The effects of the food matrix, food preparation processes and storage conditions are all factors that can influence bioactive stability and are discussed here. •Flaxseed (FX) has phytochemicals with potential cardioprotective benefits.•ALA and SDG in whole FX are stable during various domestic processes.•Exposed ALA in milled FX and FX oil increases susceptibility of oxidation.•Adding milled FX or FX oil to baked goods may improve oxidative stability.•SDG content in defatted FX flour is influenced by fermentation, but not baking.