This case study provides an account on how we struggled with the coordination of the many activities of a research project in Science Education: managing the project as a whole, collaborating on the literature review, integrating diverse research methods (interviews, classroom observation, survey), analyzing, and reporting. The initial difficulties led us to develop the concept of Digital Research Notebook, a meta-tool and set of workflows to coordinate many of these activities. We will give you practical examples of how we have developed some of the project’s research activities before and after we began using a Digital Research Notebook. We will focus on Collaboration (e.g., writing a paper collaboratively), Project management (e.g., task management), Literature review (e.g., annotating publications collaboratively), Interviews (e.g., collecting audio and handwritten notes in an integrated way), Classroom observation (e.g., a workflow to produce pedagogical graphic novels), and a Survey (e.g., making the dataset and design process open). Our aim is also to present you with scenarios through which you can reflect on the relevance of Digital Research Notebooks and envision its adaptation to your own research project.