Recent national surveys in The United Republic of Tanzania have revealed poor standards of hygiene at birth in facilities. As more women opt for institutional delivery, improving basic hygiene becomes an essential part of preventative strategies for reducing puerperal and newborn sepsis. Our collaborative research in Zanzibar provides an in-depth picture of the state of hygiene on maternity wards to inform action. Hygiene was assessed in 2014 across all 37 facilities with a maternity unit in Zanzibar. We used a mixed methods approach, including structured and semistructured interviews, and environmental microbiology. Data were analysed according to the WHO ‘cleans’ framework, focusing on the fundamental practices for prevention of newborn and maternal sepsis. For each ‘clean’ we explored the following enabling factors: knowledge, infrastructure (including equipment), staffing levels and policies. Composite indices were constructed for the enabling factors of the ‘cleans’ from the quantitative data: clean hands, cord cutting, and birth surface. Results from the qualitative tools were used to complement this information. Only 49% of facilities had the ‘infrastructural’ requirements to enable ‘clean hands’, with the availability of constant running water particularly lacking. Less than half (46%) of facilities met the ‘knowledge’ requirements for ensuring a ‘clean delivery surface’; six out of seven facilities had birthing surfaces that tested positive for multiple potential pathogens. Almost two thirds of facilities met the ‘infrastructure (equipment) requirement’ for ‘clean cord’; however, disposable cord clamps being frequently out of stock, often resulted in the use of non-sterile thread made of fabric. This mixed methods approach, and the analytical framework based on the WHO ‘cleans’ and the enabling factors, yielded practical information of direct relevance to action at local and ministerial levels. The same approach could be applied to collect and analyse data on infection prevention from maternity units in other contexts.