Modelling complex socio-environmental problems requires integration of knowledge across disparate fields of expertise. A key challenge is understanding how social learning across disciplines occurs in scientific research teams, in order that integrated knowledge is co-created. This article introduces a new framework for training researchers to integrate their knowledge across disciplines, based on current understanding of how inter- and transdisciplinary learning in research teams occurs. The framework was generated from a synthesis of learning, cognitive, and social science theories, and combines facilitated, structured negotiation processes with co-creation of boundary objects. It was used in two, 9 to 10-day intensive training workshops for doctoral students. This article describes the framework, workshop design, analysis of data collected during the workshops related to knowledge integration processes, what has been learned from the results, and the impact on participants. All participants indicated the experience was transformative, provided knowledge and skills unavailable elsewhere, filled gaps in their graduate education programs, and improving confidence in their capacity for inter- and transdisciplinary research. Pre- and post-workshop surveys confirm that the framework changed participants’ knowledge, behaviors, and competencies for engaging across disciplines. Many students have reported they have used the framework in a variety of other research and education settings, indicating they are able to transfer their new competencies to other contexts. Findings contribute to understanding of how to more effectively train researchers to integrate knowledge across disciplines for complex societal problem solving.