The bioactive compounds of four Saudi date flesh extracts (Ambara (AF), Majdool (MF), Sagai (SF), and Sukkari (SKF)) prepared using different extraction methods—namely, supercritical fluid extraction (SFE), subcritical CO2 extraction (SCE), and Soxhlet extraction (SXE)—were evaluated. A total of 19 bioactive compounds were detected in extracts prepared using SFE and SCE methods, whereas less than 12 compounds were detected in extracts obtained using the SXE method. Both the date variety and extraction method affected the phenolic profile of date flesh extract (p ≤ 0.05). The apparent viscosity, surface color, and bioactive properties of yogurt were affected by both date flesh extracts and storage duration in varied magnitudes (p ≤ 0.05). The incorporation of date flesh extracts into yogurt formulations increased the total phenolic content (TPC), DPPH antiradical activity, viscosity, and redness (a*) and decreased the lightness (L*) and yellowness (b*) of the developed product (p ≤ 0.05). The elongation of storage time progressively (p ≤ 0.05) reduced the pH, TPC, DPPH antiradical activity, bacterial counts, and L* and b* values and increased the acidity, syneresis, viscosity, and a* values with few exceptions. Date flesh extracts can improve the health quality of yogurt without major influence on the sensory attributes while stored at 4 °C.