Considerable effort has been invested in innovative practices about teaching programming. Although the usefulness of metacognition in learning process is acknowledged, evidence demonstrating how metacognitive strategies effect in the programming classrooms is still very scarce. Given the importance of metacognitive strategies, this study seeks to examine the effect of the strategies to students’ performances in programming courses. The qualitative techniques were used to determine the participants’ programming performances and explicate their experiences about the role of the strategies. The results indicated that while almost half of the students’ programming performances were multistructural the other half was prestructural and unistructural categories of Solo taxonomy. The quality of the programming problems is found to have an important role in the development of both cognitive knowledge and cognitive regulation strategies. Furthermore, the cognitive potentials and problem solving habits of the students were also found to be effective on their metacognitive development. The implications of notable findings and directions for future studies were also discussed.