Ultrasound treatment can alter the functional properties of flour systems by modifying the organization of starch, protein, lipids, and other matrix components. In this study, whole tiger nut flour (WTF) and defatted tiger nut flour (DTF) were treated with probe ultrasonication at nominal power settings of 0, 300, 600, and 900 W. Pasting behavior, gel rheology, thermal transitions, X-ray diffraction (XRD), protein electrophoretic profiles, intrinsic fluorescence, and emulsifying properties were evaluated to assess how endogenous lipids influence ultrasound-induced changes in tiger nut flour. The response to ultrasound depended on both flour type and the property measured. In WTF, peak viscosity increased at 300 W and decreased at higher power settings, whereas DTF showed a non-monotonic pasting response with partial recovery at 900 W. The storage modulus of WTF gels was highest at 600 W, whereas the rheological response of DTF was comparatively small and non-monotonic. Sonicated WTF exhibited a broad diffraction feature near 2θ ≈ 20°, which is consistent with, but does not confirm, the presence of V-type amylose-containing structures. Differential scanning calorimetry revealed high-temperature endothermic transitions whose origin could not be assigned unambiguously, because starch-related transitions, protein denaturation, water redistribution, and other matrix effects may overlap in whole-flour systems. SDS-PAGE showed no visible change in the molecular-weight distribution of the major extracted proteins. The emulsifying activity and stability of the extracted protein fractions increased up to 600 W and declined at 900 W. Collectively, the results show that endogenous lipids are associated with distinct ultrasound responses in tiger nut flour. However, the present evidence does not directly establish amylose–lipid complex formation, starch–protein complexation, or a specific lipid-mediated protein-protection mechanism; direct structural analyses are required to verify these possibilities.