Background The objective of this study was to apply systems thinking to examine the opportunities and challenges of scaling up and integrating a new electronic health technology into a complex health system. We used the implementation cycle of the supply chain management solution (SMS for Life 1.0) in Tanzania as a case study. SMS for Life was one of the earliest large-scale implementations of mHealth innovations worldwide. It aimed to bring visibility to antimalarial stock-outs through the use of SMS technology.Methods A qualitative case-study approach was used. This included a literature review, a document review of 61 project documents, a timeline of key events and the collection and analysis of 28 interviews with key stakeholders involved in or affected by the SMS for Life programme. Using the WHO mHealth Assessment and Planning for Scale (MAPS) Toolkit as a framework, we carried out a joint thematic analysis and identified the key reasons for the discontinuation of the programme.Results SMS for Life was reliable at scale and raised awareness of stock-outs with real-time monitoring. However, it was discontinued in 2015 after four years of a national rollout. The main reasons identified for the discontinuation were the programme’s failure to adapt to the continuous changes in Tanzania’s health system, the focus on stock-outs rather than ensuring appropriate stock management, and that it was perceived as costly by policy-makers.