In the Indian context, concerns have been raised for many years about the learning outcomes of primary school children (see Banerji, Bhattacharjea and Wadhwa, 2013). The complexity of the issue makes it difficult to advise stakeholders on what needs to be done to improve learning in primary schools in India. As Alcott and Rose (2017) have shown that low socioeconomic status (SES) is one of the key factors which negatively affect learning outcomes, the focus of the Multilila project ('Multilingualism and Multiliteracy: Raising learning outcomes in challenging contexts in primary schools across India') is on educational achievement among children of low SES. In following the development of language, literacy, math and cognitive abilities of primary school children over two years we hope to throw new light on why multilingual children in India do not always experience the cognitive advantages associated with multilingualism in other contexts. This paper focuses on some of the methodological challenges faced by this project. After explaining the rationale for the study in Section 1, we sketch the contribution this project can make to the discussion about cognitive advantages of bilingualism (Section 2). Section 3 focuses on the Indian context and in Section 4 we present the methodology of the project (design, participants, instruments and procedure). Finally, in Section 5 we summarize the key challenges for the project, possible solutions to those challenges and present an outlook towards the future.