PurposeThis article draws upon evidence from a contemporary study of all-through schools (ATS) in three countries. ATS combine at least two stages of a child's education in a single establishment. Many admit children aged 3–19. Most children join the school at nursery or kindergarten level and continue there for their entire education before moving on to further or higher education. ATS are also called all-age, in some contexts, because they bring children of all ages together into the same school environment. Models of ATS vary internationally; hence, there is not one definition of an ATS. This article takes a comparative look at ATS in Iceland, Spain and Wales. The purpose of this article is to explore innovative pedagogies in ATS and to explore how far deeper learning occurs because of the integrated and inclusive model of schooling. The study focused on pedagogical practices in ATS and examined how far these innovative practices are considered by teachers to foster deeper learning outcomes.Design/methodology/approachThe article draws upon a three-year comparative research project that explored pedagogy, leadership and well-being in ATS. The article investigates pedagogy with a cross-cutting focus on enquiry and deeper learning from the perspective of leaders and teachers. Using focus groups and lesson observations, a qualitative case-study approach was utilised to gather evidence about the teaching and learning processes adopted in ATS. Semi-structured interviews were also conducted with school leaders. The analytical approach adopted was one of constant comparison with the prime aim of eliciting common themes across the data sets. In relation to the pedagogy theme and an exploration of pedagogical innovation, research questions included (1) How far do ATS foster innovative pedagogies?, (2) What are the leadership conditions that support innovative pedagogies? and (3) To what extent do innovative pedagogies promote deeper learning?FindingsWithin and across the three education systems under investigation, the study found that all-through schooling engages students in a positive learning environment and provides innovative pedagogical processes associated with deeper learning. The article provides evidence about how deeper learning functions in ATS from different parts of the world and reflects on the way deeper learning is promoted by leaders and teachers, resulting in deeper learning for students. The evidence from this study reinforces that opportunities for pedagogical innovation and deeper learning within ATS occur because of flatter structures, more fluidity between different phases of learning and greater cross-over of teacher expertise. The study also highlights how leadership is a critical factor in creating the conditions for collective professional practices that foster pedagogical innovations to secure deeper learning. Findings suggest that leading for deeper learning is fundamentally concerned with creating the conditions for innovative learning environments that are equitable, inclusive, diverse and cross age ranges.Originality/valueContemporary empirical studies of the deeper learning environments within ATS remain relatively rare; hence, this study provides new comparative and contemporary evidence that illuminates the nature of the pedagogical innovation and the leadership practices that support pedagogical innovation in these schools. It also highlights how professional collaboration and cross-phase working are at the heart of innovative pedagogies that support deeper learning. The study outlined in this article provides critical, new insights about pedagogical innovation and deeper learning within ATS settings.