Demonstrated limitations in the mineral and nutritional composition of refined flours have led to calls for the possibility of enriching them with health-promoting supplements, such as high-value non-cereal seeds. Teff and watermelon seeds have been found suitable for the production of gluten-free flour, but so far, their potential to enrich conventional baking flours has not been comprehensively studied. Hence, the present study aimed at farinographic evaluation of dough based on refined wheat flour with additions of whole white teff (TF) and watermelon seed (WSF) and pomace (DWSF) flours (tested levels 10%, 20%, and 30%), as well as possibly extensive chemical characterization of the plant material tested, including LC-MS/MS, GC-MS, total phenolics, flavonoids, melatonin, and antioxidant potential. Most of the rheological traits were improved in the flour mixtures compared to the base white flour: development time and quality number (above 1.6-fold increase), softening and stability time (up to 1.3-fold change), and water absorption (up to 6%). Overall, the best results were achieved after the addition of watermelon seed pomace. The DWSF material was characterized by the highest levels of P, Mg, Na (7.5, 1.7, 0.4 g/kg, respectively), and Fe and Zn (124 and 27 mg/kg), while TF was the richest in Ca (0.9 g/kg) and Mn (43 mg/kg). Protein and fat levels were significantly higher in watermelon seeds compared to teff (about double and up to 10-fold, respectively). Phytochemical analyses highlighted the abundance of phenolics, especially flavones, in TF, WSF and DWSF flours (244, 93, and 721 mg/kg, respectively). However, the value of total polyphenols was low in all materials (<2 mg GAE/g), which also correlates with the low antioxidant potential of the samples. Watermelon seed pomace was characterized by significantly higher melatonin concentration (60 µg/kg) than teff (3.5 µg/kg). This study provides new information on the chemical composition and application opportunities of teff and watermelon seeds.