Walnut flour (WF) is a nutrient-rich source that can be used as an alternative for individuals on a gluten-free diet. This study aimed to assess the physical, chemical, and sensory changes in low-carbohydrate bread when supplemented with WF. Molecular-level changes were also examined using ATR-FTIR spectra. The bread recipe, containing buckwheat and flaxseed, was enriched with WF at levels ranging from 5% to 20%. The addition of WF resulted in increased loaf volume and decreased baking loss. Enriched bread samples showed higher protein content, while fat and available carbohydrate content decreased. Additionally, WF incorporation led to a decrease in crumb brightness and an increase in redness (from 23.1 to 25.4) and yellowness (from 23.8 to 26.7). WF also increased crumb hardness and chewiness. Moreover, the tested additives primarily influenced the intensity of FTIR spectra, indicating changes in protein, carbohydrate, and fat content, with increased band intensity observed in the protein region. We particularly recommend bread with a WF content of 15%. This type of bread is characterized by high consumer acceptance. Furthermore, compared to bread without the addition of WF, it has a higher content of phenolic compounds, protein, and fat by approximately 40%, 8%, and 4%, respectively. The antioxidant activity of this bread, determined using the ABTS and DPPH methods, is also significantly higher compared to the control bread.