Previous research has shown the validity of the Measure of Linked Concepts (MLC) assessment in college introductory chemistry. Herein, we present a novel model of pairing the MLC with a metacognitive exercise aligned with learning objectives in the introductory chemistry courses as an effective tool for instructors to be integrated into instruction and assessments. A mixed-methods approach was used to explore the effectiveness of MLCs with the metacognitive exercise on students' performance and metacognitive thinking and behaviors. The study was implemented in introductory chemistry at two institutions over two semesters. The multiple regression model showed that MLC scores significantly predicted students' final exam scores in introductory chemistry. Students' MLC scores were improved significantly (18% higher) after pairing with the metacognitive exercise. Notably, the theme of metacognition was much more prevalent observed in the qualitative data when the MLC was paired with the metacognitive exercise as compared to without the exercise (37% vs. 9%). More importantly, most of the participants (87%) reported they looked up the learning objectives that are associated with the MLC statements they missed. More than half of the participants indicated they made plans to master the missed learning objectives. Their plans include reviewing lecture notes pertaining to the topics, doing more practice problems related to the missed learning objectives, or seeking help from tutors or instructors. Pairing MLCs with the metacognitive exercise shows promising signs of improving student performance and metacognition. The authors suggest adopters of MLCs utilize the new model of pairing them with the metacognitive exercise.