This paper presents an empirical study and related activity system analysis regarding the implementation and use of Moodle specifically, and learning management systems in general, in problem-based learning. The research involved an exploration of the characteristics that defined use of Moodle at a Danish university, the reasons why Moodle was or was not used in specific contexts and the way in which Moodle use was perceived by students. Some of the obstacles and challenges identified through this study highlighted the need for a deeper analysis of the elements that characterised the activity system(s) and their contradictions in this contextual setting, leading to a consideration of possible implications for change processes. The investigation consisted of a literature review, a survey of 345 students regarding their experiences with Moodle in conjunction with a nomination for the best Moodle course, an analysis of the 178 nominated courses and interviews with four university teachers about their use of Moodle. This examination revealed that many existing Moodle activities at Aalborg University focus more on sharing information and teaching materials and less on the students' problem-based learning activities and projects. This finding is intriguing, as use of Moodle does not reflect that problem-based learning comprises the pedagogical foundation of Aalborg University's academic programme. The investigation uncovered several reasons for the lack of focus on problem-based learning in Moodle structures and content and explored them through the contradictions identified within the activity systems and between the double contextual frame surrounding the interacting activity system.