Digital knowledge maps are rich sources of information to track students’ learning. However, making sense of concept maps has been found challenging. Using multiple quantitative and qualitative methods in combination allows triangulating of changes in students’ understanding. This chapter introduces a novel form of concept map, called knowledge integration map (KIM), and uses KIMs as examples for an overview of concept map analysis methods. KIMs are a form of digital knowledge maps. KIMs have been implemented in high school science classrooms to facilitate and assess complex science topics, such as evolution. KIM analysis aims to triangulate changes in learners’ conceptual understanding through a multi-level analysis strategy, combining quantitative and qualitative methodologies. Quantitative analysis included overall, selected, and weighted propositional analysis using a knowledge integration rubric and network analysis describing changes in network density and prominence of selected concepts. Research suggests that scoring only selected propositions can be more sensitive to measuring conceptual change because it focuses on key concepts of the map. Qualitative analysis of KIMs included topographical analysis methods to describe the overall geometric structure of the map and qualitative analysis of link types. This chapter suggests that a combination of quantitative and qualitative analysis methods can capture different aspects of KIMs and can provide a rich description of changes in students’ understanding of complex topics.