The addition of flaxseed and amaranth on the physicochemical, functional and microstructural changes of instant-extruded cereals was evaluated. Six different mixtures were made with additions of amaranth (30%–50%) and flaxseed (10% and 15%) using maize grits and minor additives as supplementary ingredients and then extruded in a twin-screw extruder. The extrudates evaluated, had insoluble and soluble fiber contents increased with the proportion of amaranth and flaxseed. The mixture 4 (higher flaxseed content) presented highest soluble fiber percentage (1.9%). Extruded cereals had the lowest viscosity (<99.5 cp) and highest hardness values (5.2 N) whereas the dietary fiber content was highest. Fiber content increase, resulted in a higher water solubility index (WSI) (0.5) and decrease the water absorption index (WAI) (2.5). Amaranth and flaxseed incorporation increased crystallinity, resulting in a larger, and more compact laminar structure. Amaranth and flaxseed addition resulted in extruded cereals with acceptable physicochemical and functional properties.