The Gender and Adolescence: Global Evidence programme is a decade long cross-country longitudinal study of adolescents in low- and middle-income countries. The programme’s large sample size and variety of contexts make it an important case study of how to deal with large and complex qualitative datasets. In this methodological article, we explore some of the challenges and opportunities that occur when working with large datasets of longitudinal qualitative research. We provide examples of lessons learnt during GAGE data collection, coding, analysis and data management. This paper also explores the use of the qualitative data analysis software MAXQDA for simplifying the analysis of longitudinal data and providing opportunities for novel analytical techniques. We find that large longitudinal qualitative datasets can provide extremely rich and detailed data; however, there needs to be attention to key processes to ensure rigour and effectively utilise the breadth and depth of the data. These include mechanisms to work effectively with large teams of researchers, strong data management and coding procedures, and using qualitative software to manage and simplify data.