It becomes increasingly clear that the relationship between structure and function of hierarchical biominerals can only be understood by connecting the length scales and interrogating comprehensively the impact of atomic-level organisation and the multi-level assembly of the resulting composites. This Faraday Discussion focuses on the application of advanced methods to scrutinise existing paradigms in biomineralisation and improve our understanding of mineralisation across length scales by bringing together different communities including world-leading experts in relevant imaging and spectroscopy techniques with the biomineralisation community where these methods are commonly used.