The study aimed to develop protein- and fiber-enriched cookies by partially substituting wheat flour with soy flour and oats. Four formulations (S1–S4) were prepared with varying substitution levels to assess their nutritional, functional, sensory, and microbiological qualities. The formulation S4 exhibited the highest nutrient composition, including protein (16.79%), fat (12.65%), and fiber (4.82%), along with elevated mineral contents zinc (2.35 mg/100 g), iron (5.79 mg/100 g), magnesium (116.20 mg/100 g), and calcium (91.73 mg/100 g). Phytochemical analysis revealed that S4 also contained the greatest flavonoid (0.54 mg QE/g) and phenolic (0.18 mg GAE/g) concentrations, as well as the highest DPPH radical scavenging activity (55.04%). Among sensory parameters, S2 was most preferred for color, flavor, taste, and overall acceptability. After one month of storage, S4 demonstrated the lowest total viable count, indicating good microbial stability. Overall, the incorporation of soy flour and oats significantly enhanced the nutritional and antioxidant properties of cookies, suggesting their potential as functional and health-promoting snack alternatives.