This study aims to validate and refine the Metacognitive Skills Questionnaire (MCSQ) to assess the impact of AI applications on university students’ cognitive processes. Through meticulous scale development and validation procedures, a 16-item version of the MCSQ was established with favorable psychometric properties. The study employed a cross-sectional design, recruiting university students from South India as participants. Results indicate that the shortened MCSQ demonstrates good reliability and validity, making it suitable for measuring metacognitive skills amidst AI usage. However, limitations include the lack of longitudinal data and sample homogeneity. Future research should explore longitudinal effects and include diverse populations to enhance generalizability. This study lays the groundwork for investigating the dynamic relationship between AI and metacognition, offering a valuable tool for educators and policymakers to optimize AI-assisted education and foster cognitive growth in the digital age.