BACKGROUND: Malaria remains a significant public health problem in Guinea-Bissau, West Africa. Government control measures include bed net distribution campaigns, however, local knowledge, attitudes and practices towards bed nets and malaria are uncharacterized on the remote Bijagos Archipelago. METHODS: Knowledge, attitude and practice questionnaires were conducted with household heads, aiming to explore the understanding of malaria and factors influencing bed net uptake and usage. Nets were observed in situ to appraise net quality and behaviour. All 14 villages and one semi-urban neighbourhood on Bubaque Island were included. One in 5 households containing school-aged children were randomly selected. RESULTS: Of 100 participants, 94 were aware of malaria and 66 of those considered it a significant or severe problem, primarily because of its impact on health and income. Transmission, symptoms and risk factors were well known, however, 28.0% of participants felt under-informed. Some 80.0% reported contact with distribution campaigns, with inter-village variability. Campaign contact was associated with feeling well informed (OR 3.44; P = 0.024) and inversely with perceiving malaria a household (OR 0.18; P = 0.002) or regional problem (OR 0.25; P = 0.018). Every household contained nets; every identifiable example was a long-lasting insecticide-treated net (LLIN), however, 23.0% of households contained at least one expired net. Replacements were in demand; 89.0% of households reported that all residents used nets, and average occupancy was 2.07 people per net; 65.2% stated that the repurposing of bed nets was common. Correctly using bed nets, defined by age, integrity and demonstration, was 35.0% and strongly associated with completing intermittent preventative treatment in pregnancy (RR 3.63; P = 0.014). CONCLUSIONS: Knowledge of malaria is good in these communities. Bed nets are used widely and are valued for their role in preventing malaria. However, their use is frequently sub-optimal and offers a target for improving malaria control by adapting popular distribution campaigns to provide more education alongside fresh LLINs. The impact of this could be significant as LLINs represent the mainstay of malaria prevention in Guinea-Bissau; however, the persistence of malaria despite the high uptake of LLINs seen in this study suggests that novel supplementary approaches must also be considered.