Background Hygiene behaviour change programmes are complex to design. These challenges are heightened during crises when humanitarian responders are under pressure to implement programmes rapidly despite having limited information about the local situation, behaviours and opinions – all of which may also be rapidly evolving. Methods We conducted in-depth interviews with 36 humanitarian staff involved in hygiene programme design in two crisis-affected settings – one a conflict affected setting (Iraq) and the other amid a cholera outbreak (DRC). Interviews explored decision-making in each phase of the humanitarian project cycle and were thematically analysed. Results Participants considered the design and implementation of hygiene programmes in crises to be sub-optimal. Humanitarians faced sector-specific challenges as well as more general constraints associated with operating within the humanitarian system. Programme-design decisions were made naturalistically and relied heavily on the intuitions and assumptions of senior WASH staff. National organisations were often side-lined from programme design processes despite being in a better position to gather situational data. Consequently, programme design and decision-making processes adopted by humanitarians were similar across the two settings studied and led to similar types of hygiene promotion activities being delivered. Conclusion Hygiene programming in crises-affected settings could be strengthened by initiatives targeted at supporting humanitarian staff during the pre-implementation programme design phase. This may include rapid assessment tools to better understand behavioural determinants in crisis-affected contexts; the use of a theory of change to inform the selection of programme activities; and funding mechanisms which encourage equitable partnerships, phased programming, regular adaptation and have programmatic components targeted at sustainability and sector capacity building. Initiatives aimed at sector reform should be cognisant of inter and intra-organisational dynamics, the ways that expertise is created and valued by the sector, and humanitarian habits and norms that arise in response to system constraints and pressures. These micro-organisational processes affect macro-level outcomes related to programme quality and acceptability and determine or limit the roles of national actors in programme design processes.