There have been several calls for more transparency in realist methods, particularly in the complex process of programme theory development and refinement. This paper will describe the way in which Computer Assisted Qualitative Data Analysis Software, specifically, NUD*IST Vivo (NVivo), was used to build and refine programme theories (using literature and interview data) in a realist evaluation. This article presents the evolving and complex process of coding several data sources to nodes and child nodes, whilst writing 'attached memos' to highlight the process of theory generation. In this project, NVivo helped create an explicitly documented and evidenced audit trail of the process of programme theory refinement, answering to calls for further transparency in realist analysis. RAMESES I and II have provided a platform to improve transparency in reporting realist research, by developing consensus and evidence-based reporting guidelines. We propose that the use of NVivo in realist approaches can help structure the iterative and by nature 'messy' process of generating, refining and testing complex programme theories when drawing on multiple data sources simultaneously. This effectively creates a structured track record of the analytical process, which increases its rigour and transparency.