The development of technology and current conditions has enabled the diversification of studies on the foods, cooking techniques, and their effects on food composition. One of the emerging cooking methods in this context is molecular cooking, which is applied across various food categories, and offers numerous advantages beyond enhancing the appearance and taste of foods. Techniques such as sous vide, foaming, spherification, use of liquid nitrogen, powdering, flavor-aroma transfer, smoking, gelling, and ultrasonic application techniques are widely used in molecular gastronomy. The application of these cooking techniques can support consumer health by positively affecting the phenolic components and total antioxidant capacity of different foods, as well as promoting innovation in the food industry and presenting foods to consumers with attractive presentations. Moreover, molecular cooking techniques have the potential to innovate and transform the functional compounds of foods, diverging from traditional methods. These changes can significantly impact human health, necessitating a comprehensive evaluation and strategic approaches. This review investigates the effect of molecular cooking techniques on the functional compounds. Recent studies indexed in major databases were analyzed, and the data were systematically organized into tables, offering insights into the role of these techniques in shaping food composition.