The article discusses methodological procedures and challenges in a project requiring multi-site, transnational data collection for the construction of a corpus of academic writing in EMI higher education contexts. Drawing on our decision-making experiences as a research team, together with empirical data generated through data collection logs recorded by a network of researchers involved in the project, we reflect on key issues in conducting the project and the solutions we found to address specific challenges. After describing the background to the project and the current status of the corpus, we focus on four broad challenges: (1) selecting partners and managing a multi-site project; (2) defining a working construct of academic writing; (3) categorising data according to disciplinary areas; and (4) managing data collection “on the ground”. Throughout, we provide descriptions of our solutions to the challenges identified, and we conclude with a call for further publication of corpus construction records to provide greater transparency and detail around decisions and judgements made at all stages of a corpus construction project.