The aims of this paper are to describe the development of an intervention to improve teamwork and systems in general practice that support the care of patients with diabetes, ischaemic heart disease and hypertension and to identify the challenges to implementing the intervention. Effective teamwork in general practice encompasses general practitioners (GP), clinical and non-clinical staff, each with clearly defined roles and opportunities to provide feedback and input into how the practice is run and chronic disease managed. The intervention implemented in this study provided an opportunity for key members of general practice teams to work with a facilitator on changes to improve teamwork over three practice visits over 6–12 months. Facilitators had experience in practice support and goal setting, an understanding of the Medicare Items and knowledge about teamwork and systems. The visits focussed on the specific needs and capacities of each practice, assisting the team to set manageable goals and building systems that best utilise the systemic and human resources available. Successful implementation of sustained change depended on strong leadership in the practice and cooperation between team members as well as clear and achievable goals being set. Structured facilitation of teamwork in general practice should focus on goal setting and the development of leadership and communication rather than delivery of information or resources.