This study aims to investigate properties of whole wheat flour breads produced with the combined addition of amaranth (5, 10, and 15%) and fennel (1, 1.5, and 2%) powders. The color, texture, total phenolic content, and sensory properties of breads were determined in terms of quality and functional properties evaluation. The protein contents of whole wheat flour and amaranth powder were found as 11.55 and 13.89%, respectively. The close protein ratios, low substitution levels and simultaneous substitution of fennel powder with amaranth did not cause significant changes in protein ratios of breads. In addition, amaranth (2.36%) and fennel (7.04%) powders contain higher ash content to whole wheat flour (1.53%), and ash ratios of breads containing 10% amaranth–1.5% fennel and 15% amaranth–2% fennel increased significantly and were determined as 3% and 3.14%, respectively. The fennel also significantly increased phenolic content of bread, with a total phenolic content of 3989.19 mg GAE/100 g DW in 2% fennel-containing bread, compared to 2750.99 mg GAE/100 g DW in control bread. The darkness of crust and crumb increased with the increase in amaranth and fennel ratio. While the whiteness index of crumb decreased from 43.65 to 36.14, the browning index of crust increased from 78.36 to 92.17 with increasing substitution level. The using of gluten-free powders also affected textural properties of samples, and hardness of breads increased when amaranth and fennel ratio increased. While all breads were found acceptable in sensory evaluation, bread containing 10% amaranth and 1.5% fennel was defined as the most acceptable.