Researching motivation in language learning is complex and multi-faceted. Various models of learner motivation have been proposed in the literature, but no one model supplies a complex and coherent framework for investigating a range of motivational characteristics. Building on previous models I propose such a methodological framework, based on a complex dynamic systems perspective, which re-conceptualises the investigation of motivation in second language acquisition in qualitative and mixed method approaches by offering one flexible tool for case study approaches. This new framework has been tried and tested in three locations in England and reported as case studies. The study aimed to address the following research questions: (1) In what ways does content and language integrated learning (CLIL) impact on learner motivation? (2) What are the main elements of CLIL that enhance motivation? Overall analysis of the results found that where expectations of success were high and where the teaching was effective, CLIL had a positive impact on motivation and progress. The framework is designed to be flexible enough to be used to investigate language learning in a range of national contexts. It is hoped that the proposed framework, reported here together with exemplification and commentary from the English study, will enable researchers in a wide range of language learning contexts to investigate learner motivation in a systematic and in-depth manner.