In the late 1990s an international feminist network, Gender at Work, wrote about the ‘deep structure’ of organisations through which gender discriminatory norms and power relations are reproduced. In this article, the authors reflect on the evolution since the Fourth World Conference on Women held in Beijing in 1995 of Gender at Work's theory and practice on approaches to shift deep structure. The Gender at Work Analytical Framework, used by dozens of organisations worldwide to assess, strategise and evaluate the process of organisational change, is described. Using a case study on the Dalit Women's Livelihood Accountability Initiative in Uttar Pradesh, India, the article demonstrates the adaptation of the Analytical Framework for working directly with community-level programmes, highlighting its strength at bringing into focus the deeply entrenched social norms and deep structures that exclude women from claiming their rights. The article concludes with reflections on what Gender at Work has learned since Beijing about working to challenge deep structures in organisations, programmes and systems.