Background: This study aimed to determine the effect of poppy seed flour (PF) on the physicochemical and spectroscopic properties of low-carbohydrate, high-protein, and gluten-free bread. Methods: The changes at the molecular level were assessed in bread using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). Bread prepared with buckwheat, flaxseed, and pea protein was enriched with PF at a concentration of 5–15%. Results: The results showed that the pasting parameters of dough supplemented with PF were significantly decreased compared to the control sample. The obtained bread samples were characterized by good quality and had 14.6% of carbohydrate, 16.3% of protein, 10.2% of fiber, and 4.0% of fat, with a caloric value of 177 kcal/100 g. The addition of PF had little influence on crumb mechanical properties. The ATR-FTIR analyses revealed spectral changes in the region related to protein and carbohydrate structures, as well as changes in band intensity characteristic of α-1,4-glycoside and α-1,6-glycoside bonds. The analyses showed that the main starch skeleton remained clearly visible. Conclusions: PF up to 10% can be potentially applied as a functional ingredient in the production of bread based on buckwheat and linseed flour. Such low-carbohydrate bread can be particularly useful to diabetics