Provided are methods for preparing, and compositions comprising, plant-based forms of omega-3 fatty acids and lignan, which methods and compositions are exemplified by methods for preparing roasted seed granules, including roasted flaxseed granules, and compositions that comprise one or more roasted seed granules that are prepared by roasting and grinding under specified conditions of temperature and time, as disclosed in detail herein, to enhance one or more desired properties including the digestibility and/or palatability of such seeds and/or the bioavailability and/or stability of omega-3 and other fatty acids that are constituents of those seeds.