Background: In cystic fibrosis care, patients are required to adhere to a burdensome daily treatment regimen. The outpatient cystic fibrosis clinic presents an opportunity for multidisciplinary healthcare teams to monitor disease progression, support daily treatment adherence, address adherence challenges and improve health outcomes. However, the complexity of adherence care, and inconsistencies in methods and delivery of adherence interventions may impact the effectiveness of healthcare teams changing adherence outcomes. Comprehensive adherence protocols have been proposed (CF My Way) to increase the visibility, consistency and efficacy of adherence work. Barriers in the clinic environment have been implicated in their unsuccessful translation into standard care. The aim of this study was to explore the feasibility, acceptability and appropriateness of implementing the ‘CF My Way’ protocol into the outpatient cystic fibrosis clinic of a tertiary, paediatric hospital Methods: This implementation study employed a pre-post observational study design using mixed methods. A four-phased implementation framework guided the implementation plan. Prior to the program introduction, qualitative data was collected from 23 clinicians, adolescents and parents using focus groups and interviews to identify barriers and enablers to implementation. Quantitative data was collected using purpose-designed audit tools and surveys throughout the implementation and analysed to inform modifications and support translation to standard care. Discussion: Theoretically and conceptually-derived implementation science frameworks can inform the process of translating an adherence protocol into an existing CF healthcare setting. Results indicate that while using an adherence protocol is acceptable and appropriate according to the perspectives of clinicians and parents, ‘CF My Way’ is not yet an “off the shelf” solution to the adherence challenge. Modifications were required to the original adherence protocol to support integration. Implementation strategies such as pilot testing, systems analysis and team cultural interventions are indicated to support effective and consistent adherence care pathways in the CF clinic. Trial registration number: ACTRN12619001730190 Trial web address: http://www.ANZCTR.org.au/ACTRN12619001730190.aspx