Abstract Background Malaria preventive measures, including long-lasting insecticide-treated bet nets (LLINs), indoor residual spraying (IRS), and controlling mosquito breeding sites, are key measures to achieve malaria elimination. Still, compliance with these recommended measures remains a major challenge. By applying a novel and comprehensive model for determinants of malaria prevention behaviour, this study tests how individual perceptions influence the intentions to use malaria preventive measures and explores strategies that stimulate their consistent use. Methods The study was carried out in the sectors of Ruhuha and Busoro, Rwanda during October and November 2017, and these were conducted into two phases. Phase one involved a questionnaire survey (N = 742), whereas Phase two employed a qualitative approach that included nine focus group discussions, seven key informant interviews, and three in-depth interviews. Results The findings of the quantitative study showed that participants very often use LLINs (66.6%), accept IRS (73.9%), and drain stagnant water in case of presence (62%). The intentions to use malaria preventive measures were consistently driven by perceived severity, perceived self-efficacy, perceived response efficacy, and subjective norms, and hindered by perceived barriers. The intentions were also positively associated with the actual use of LLINs, acceptance of IRS, and drainage of stagnant water. There is no evidence that either not having enough LLINs (ownership of at least one bed net in the household, here referred to as availability) or having sufficient LLINs (having one LLIN per two people in the household, here referred to as accessibility) moderated the relationship between behavioural intentions and actual use of LLINs. The qualitative study indicated that participants believed malaria risk to be high and perceived a high mosquito density. They also believed that repetitive malaria episodes are caused by the perceived low effectiveness of anti-malaria medications. Lack of LLINs increased the perceived added value of LLINs, and together with the increased malaria burden increased the perceived response efficacy. Participants highlighted the need to continuously mobilize and engage community members especially those who do not use LLINs when having one, and those who do not accept the spraying activities. Conclusion Malaria prevention interventions should target individual perceptions to enhance consistent use of malaria preventive measures. Three strategies to improve consistent use and acceptance of these measures are highlighted: (1) ensure access to LLINs and regular spraying activities, (2) community mobilization and (3) citizen engagement in malaria prevention activities.