Developed nations are implementing initiatives to transform the delivery of primary care. New models have been built around multidisciplinary teams, information technology and systematic approaches for chronic disease management (CDM). In Australia, the General Practice Super Clinic (GPSC) model was introduced in 2010. A case study approach was used to illustrate the development of inter-disciplinary CDM over 12 months in two new, outer urban GPSCs. A social scientist visited each practice for two 3-4-day periods. Data, including practice documents, observations and in-depth interviews (n≤31) with patients, clinicians and staff, were analysed using the concept of organisational routines. Findings revealed slow, incremental evolution of inter-disciplinary care in both sites. Clinic managers found the facilitation of inter-disciplinary routines for CDM difficult in light of competing priorities within program objectives and the demands of clinic construction. Constraints inherent within the GPSC program, a lack of meaningful support for transformation of the model of care and the lack of effective incentives for collaborative care in fee-for-service billing arrangements, meant that program objectives for integrated multidisciplinary care were largely unattainable. Findings suggest that the GPSC initiative should be considered a program for infrastructure support rather than one of primary care transformation.