Complementing traditional food processing techniques with emerging ones like three-dimensional (3D) food printing can re-innovate the derived products as more consumer-centric with known human wellness values. This study investigated the nutritional quality, polyphenol composition, and antioxidant activity of conventional and 3D printed biscuits from the same wholegrain and multigrain flours. Fermented cowpea and germinated quinoa were bioprocessed at 28 °C for 48 h and freeze-dried to obtain cowpea sourdough and malted quinoa flours, and the flours subsequently used to prepare kneaded and shaped dough or 3D printed dough baked as biscuits. Some chemical compositions of the biscuits revealed minute differences in ash, fiber, protein, threonine, serine, as well as potassium content and significant differences (p ≤ 0.05) in total flavonoid contents and phenolic compounds. The 3D printed biscuits from biomodified flours had improved concentrations of methionine, aspartic, glutamic, higher iron and phosphorus contents, slightly varied antioxidant activities, and better appearances than the corresponding conventional biscuits. The comparable and improved chemical compositions of the 3D printed biscuits indicate the possible use of value-added intermediate products from traditional processing techniques with emerging technology to manufacture in-demand novel foods with wellness-promoting properties beyond basic nutrients.