Large-scale implementations of effective inquiry-based learning are rare. A European-wide initiative gave teachers access to innovative e-learning tools (ranging from virtual labs, virtual games and simulations to augmented reality applications) for lesson planning and classroom implementation. We examined 668 such implementations across 453 schools within the period of one school year. Teachers could use a platform with digital resources and tools and were encouraged to adopt five different phases of inquiry-based learning: orientation, hypothesizing, planning, analysis, and conclusion. Additionally, an integrated interface for lesson implementation tracked each students’ problem-solving competence (during the inquiry lessons), culminating in about 12,000 datasets. Every user generated an average of 22 digital inquiry-based digital scenarios, each of which required approximately 50.14 min for completion. These scenarios, using high quality resources adapted to school conditions, yielded significant learning outcomes for participating students (age: 14.4 years, gender balanced). While the PISA study identified 10% high achievers on average, we exceeded this number in our framework scoring 20–29% high achievers and 37–42% low achievers (which was close to the 45% PISA average). Offering tools to teachers, which help creating individual inquiry scenarios and monitoring students’ achievement, does not yield any insurmountable obstacles for classroom-implementation of inquiry-based lessons: Compared to the PISA study, levels of high achievers increased even if complex problem-solving competence was required.