Background Adaptation of daily behaviours can play a significant role in disease prevention. Behaviour Insight Shadowing (BIS) is a novel qualitative methodology, designed and used for the first time in this study, which applies the Behaviour Settings Theory as a framework for interrogating daily life patterns and identifying optimal opportunities for behaviour change. Methods Nine participant households were shadowed for a day, in Nigeria, the Democratic Republic of Congo and Guinea Bissau. Shadowing involved close ethnographic observation alongside integrated interviewing techniques, and then followed up with a semistructured cross-examination at the end of the observation period. Real-time insights about the attitudes and behaviours of households at high risk of neglected tropical diseases (NTDs) were then categorised by context and analysed thematically. Themes were then applied to a framework of understanding specific to NTD behaviour change and therefore informing more effective social behaviour change communications (SBCC) design. The methodology is adaptable, simple to replicate and produces in-depth, qualitative ethnographic stories. Results Findings highlighted important spatial and temporal aspects of target behaviours, with key differences between private and group activities. Ethnographic stories illustrated hierarchies between economic, social and temporal drivers of behaviour, and highlighted the ways in which health messages were introduced and responded to within and between households. This provided cultural levers for more impactful SBCC interventions that could tie into existing norms. Conclusions BIS methodology, as an adaptive ethnographic approach, provides valuable insights that enhance the findings from surveys and focus groups, specifically in the context of NTD prevention. Contextual categorisation of relevant daily behaviours is key to developing culturally appropriate SBCC and in determining whether such intervention needs to be in alignment with everyday routines and attitudes, or in disruption of them.