Metacognition plays a significant role in student learning, especially in solving ill-structured problems. Computer science students who are enrolled in a software engineering course or information systems development projects have to complete ill-structured problems, in this case a project that can be solved using more than one solution or approach. Although the course is compulsory, it is important to understand its implementation from cognitive/metacognitive perspective. The objective of the study is to investigate the students' metacognitive skills while working on their information systems projects. We used Engineering Design Metacognitive Questionnaire (EDMQ) as the instrument that is grounded in Butler and Cartier's self-regulated learning (SRL) model. Two early phases in design phases were used, namely Problem Definition and Conceptual Design. One hundred and thirty-four students enrolled in IS Development Project course at Faculty of Computer Science, Universitas Indonesia participated in the study. There are two types of data collected in the study, quantitative and qualitative data. The results found that on average the students often employ metacognitive skills under the following categories: Task Interpretation, Planning Strategies, Cognitive Actions, Monitoring and Fix-Up strategies, and Criteria of Success.