Abstract Background Health literacy (HL) affects how individuals engage in preventive behaviours, seek prompt treatment, select appropriate malaria prevention or treatment options, adhere to care and act on health information. Little is known about its role in malaria prevention and treatment behaviours. Therefore, this study investigated the extent to which HL relates to malaria health behaviours. Methods A cross-sectional household survey across urban and rural areas of Gabon using a sample of 504 respondents. HL was measured using the French HLS-EU-Q16 and scored as well as categorised as inadequate, problematic, or sufficient. Malaria health behaviours included regular utilisation of bed nets, uptake of indoor residual spraying (IRS), treatment-seeking for illness, medication adherence, bush clearing, asking medical practitioners questions and Dosage knowledge. The HL scale was first assessed for psychometric suitability within the study sample before conducting subsequent regression analyses. Multivariable logistic regression models were employed to assess associations between HL and malaria-related behaviours, with adjustment for demographic, socioeconomic, and health-environment factors. Results 59.7 per cent of respondents demonstrated sufficient HL with higher proportions among those with at least secondary education (above 65%), urban residents (61.4%), those aged between 25 and 34 years of age (66.4%) and those using formal health information sources (60.2%). Significant bivariate associations were revealed between HL and dosing knowledge, medication adherence, prompt treatment seeking and asking questions. No bivariate associations were observed for Bednet use or bush clearing. However, multivariate logistic regression adjusting for demographic, socio-economics and health environment factors revealed significant associations of HL with dosing knowledge (AME = 0.022, p < 0.001), medication adherence (AME = 0.013, p < 0.01; OR = 1.089), asking questions (AME = 0.018, p < 0.001; OR = 1.092), and bednet use (AME = 0.012, p < 0.05). Treatment-seeking behaviours, bush clearing and indoor spraying were not significantly associated with HL ( p > 0.05). Conclusion HL has associations with knowledge-dependent and communicative aspects of malaria management. Therefore, literacy-focused interventions in malaria-endemic regions should be prioritised alongside structural approaches addressing net access and healthcare availability to maximise impact on malaria-related outcomes. Clinical trial number Not applicable.