This article describes experiences with a qualitative research project into teachers' learning from innovating their own educational practices. Decades of New Public Management (NPM) in the Netherlands, with its top-down and businesslike approach to areas of public interest, obscured the learning and innovating capacity of teachers, teams, and schools. Merely studying the learning processes which take place at a teacher level would present insufficient insight into the deeper mechanisms which hinder or stimulate learning from innovation in a bottom-up manner. We, therefore, focused on the relations between different layers (individual, systemic) within schools. A high-quality design was required for answering the research question: How and what do teachers learn from innovating their own educational practices? This article elaborates upon this design and discusses the methodological findings and complications of this type of research.