Making sense of concept maps is an ongoing challenge for the concept mapping community. This paper introduces a multi-level analysis strategy by combining quantitative and qualitative methods to triangulate changes in students’ concept maps. Quantitative analysis includes overall, selected, and weighted propositional analysis using a knowledge integration rubric (Linn, 2000) as well as network analysis to describe changes in network density and prominence of selected concepts. Research suggests that scoring only selected propositions can be more sensitive to indicate conceptual change because it focuses on key concepts of the map. Qualitative analysis includes topographical analysis methods to describe the overall geometric structure of the map and an analysis of link types. This paper suggests that a combination of quantitative and qualitative analysis methods can capture different aspects of concept maps and provide a rich description of changes in students' understanding of complex topics.