Background Long-lasting insecticidal nets (LLIN), indoor residual spraying (IRS) and malaria case treatment with artemisinin-based combination therapy (ACT) have been proven to significantly reduce malaria, but may not necessarily lead to malaria elimination. This study explored factors hindering the acceptability and use of available malaria preventive measures to better inform area specific strategies that can lead to malaria elimination. Methods Nine focus group discussions (FGD) covering a cross-section of 81 lay community members and local leaders were conducted in Ruhuha, Southern Eastern Rwanda in December 2013 to determine: community perceptions on malaria disease, acceptability of LLIN and IRS, health care-seeking behaviours and other malaria elimination strategies deployed at household and environmental levels. Discussions were recorded in Kinyarwanda, transcribed into English and coded using Nvivo 10 software. Results Participants ranked malaria as the top among five common diseases in the Ruhuha sector. Participants expressed comprehensive knowledge and understanding of malaria transmission and symptoms. The concept of malaria elimination was acknowledged, but challenges were reported. Sleeping under a bed net was negatively affected by increase of bedbugs (and the associated irritability) as well as discomfortable warmness particularly during the dry season. These two factors were reported as common hindrances of the use of LLIN. Also, widespread use of LLIN in constructing chicken pens or as fences around vegetable gardens was reported. Participants also reported that IRS appeared to lead to an increase in number of mosquitoes and other household bugs rather than kill them. Prompt health centre utilization among participants with presumed malaria was reported to be common particularly among subscribers to the subsidized community-based health insurance (CBHI) scheme. In contrast, the lack of CBHI and/or perceptions that health centre visits were time consuming were common reasons for the use of over-the-counter medicines for malaria management. Conclusion In this study, identification of behavioural determinants in relation to LLIN use, IRS acceptability and health care seeking is a critical step in the development of effective, targeted interventions aiming to further reduce malaria transmission and elimination in the area.