Background Widespread vector control has been essential in reducing the global incidence and prevalence of malaria, despite now stalled progress. Long-lasting insecticide-treated nets (LLINs) have historically been, and remain, one of the most commonly used vector control tools in the campaign against malaria. LLINs are effective only with proper use, adherence, retention and community adoption, which historically have relied on the successful control of secondary pests, including bed bugs. The emergence of pyrethroid-resistant bed bugs in malaria-endemic communities and failure to control infestations have been suggested to interfere with the effective use of LLINs. Therefore, the behavioral interactions of bed bugs with commonly used bed nets should be better understood. Methods To investigate the interactions between bed bugs (Cimex lectularius L.) and LLINs, insecticide-susceptible and pyrethroid-resistant bed bugs were challenged to pass through two commonly used LLINs in two behavioral assays, namely host (blood meal)-seeking and aggregation-seeking assays. The proportions blood-fed and aggregated bed bugs, aggregation time and mortality were quantified and analyzed in different bed bug life stages. Results Overall, both the insecticide-susceptible bed bugs and highly resistant bed bugs showed a varying ability to pass through LLINs based on treatment status and net design. Deltamethrin-treated nets significantly impeded both feeding and aggregation by the susceptible bed bugs. While none of the tested LLINs significantly impeded feeding (passage of unfed bed bugs through the nets) of the pyrethroid-resistant bed bugs, the untreated bed net, which has small mesh holes, impeded passage of fed bed bugs. Mortality was only seen in the susceptible bed bugs, with significantly higher mortality on deltamethrin-treated nets (63.5 ± 10.7%) than on permethrin-treated nets (2.0 ± 0.9%). Conclusions Commonly used new LLINs failed to prevent the passage of susceptible and pyrethroid-resistant bed bugs in host- and aggregation-seeking bioassays. The overall low and variable mortality observed in susceptible bed bugs during both assays highlighted the potential of LLINs to impose strong selection pressure for the evolution of pyrethroid resistance. Already, the failure to control bed bug infestations has been implicated as a contributing factor to the abandonment or misuse of LLINs. For the first time to our knowledge, we have shown the potential of LLINs in selecting for resistant secondary pest populations and so their potential role in stalling malaria control programs should be further investigated. Graphical Abstract The emergence of pyrethroid-resistant bed bugs in malaria-endemic communities may interfere with the effective use of pyrethroid-impregnated bed nets. We assessed the interactions of two bed bug strains with commonly used bed nets using two behavioral assays, namely host (blood meal)-seeking by unfed bed bugs and aggregation-seeking by freshly fed bed bugs. These assays assessed the passage of bed bugs through various bed nets in response to host cues and aggregation stimuli, respectively. Conditioned paper is a section of file folder paper that has been exposed to bed bugs and has been impregnated with feces and aggregation pheromone; it is attractive to aggregation-seeking fed bed bugs. An unconditioned ramp is a similar section of file folder paper that allows bed bugs to traverse the bed net and gain access to a blood-meal source.