This study investigates and analyzes learning phenomena related to moral values in the content of problem-based learning activities, the process of moral values internalization in relation to problem-based learning situations, conditions that relate to the enhancement of comprehension as well as internalization of the values, and their impact to the tendency of actualizing the values into better student behaviour. This research was conducted with participation of the students of the Arabic Department, Faculty of Language and Arts Education, Indonesia University of Education in the academic years 2009, 2010, and 2011. The data to be analyzed in this research comprises of the students' written responses (initial responses, group work responses, and written reflection), classroom observation, and in-depth interviews. The data used was analyzed by considering the principles of credibility, dependability, transferability and confirmability. Data analysis, using principles of qualitative approach, reveals phenomena relating to the students' comprehension, feelings, and behavior regarding the moral values, as a result of learning stages designed based on the theoretical framework. In addition to this result, an instructional theory and a learning theory can be formulated.