Mushrooms, due to their basic composition and the presence of numerous mycochemicals, can be used to improve various food matrices. The objective of this study was to determine the impact of replacing wheat flour (2%, 4%, 6% w/w) with mushroom lyophilisates from cultivated mushrooms—A. bisporus and P. ostreatus—on the technological quality, basic nutritional and elemental composition, antioxidant activity (ABTS, FRAP), total polyphenol content (TPC), and sensory evaluation of shortbread cookies. The functional properties of blended flours were also determined, such as bulk density (BD), water- and oil-holding capacity (WHC, OHC), swelling capacity (SW), and water solubility index (WSI). The results show that the amounts of protein, fiber, and ash were higher in cookies enriched with mushrooms than in control cookies. The enriched products, depending on the amount of mushroom powder used and the mushroom species, had a higher content of zinc, iron, magnesium, potassium, and copper. The increase in the addition of mushroom powder resulted in a significant (p < 0.05) increase in the TPC content and antioxidant properties. The use of composite flours contributed to a significant increase in hardness (at 6% mushroom powder) and a change in color parameters, with lower whiteness and a greater ΔE recorded for cookies with A. bisporus lyophilisate. In the sensory evaluation, the samples enriched with P. ostreatus powder received higher scores compared with control samples, while the cookies with A. bisporus flour were evaluated lower than the control.