BACKGROUND: The control of malaria in pregnancy in much of Asia relies on screening asymptomatic women for malaria infection, followed by passive case detection and prevention with insecticide-treated nets. In 2012, Indonesia introduced screening for malaria by microscopy or rapid diagnostic tests (RDTs) at pregnant women's first antenatal care (ANC) visit to detect and treat malaria infections regardless of the presence of symptoms. Acceptability among health providers and pregnant women of the current 'single screen and treat' (SSTp) strategy compared to two alternative strategies that were intermittent preventive treatment (IPTp) and intermittent screening and treatment (ISTp) was assessed in the context of a clinical trial in two malaria endemic provinces of Eastern Indonesia. METHODS: Qualitative data were collected through in-depth interviews with 121 health providers working in provision of antenatal care, heads of health facilities and District Health Office staff. Trial staff were also interviewed. Focus group discussions were conducted with 16 groups of pregnant women (N = 106) to discuss their experiences of each intervention in the trial. RESULTS: Health providers and pregnant women were receptive to screening for malaria at every ANC visit due to the increased opportunity to detect and treat asymptomatic infections. A primary concern for providers was the accuracy and availability of RDTs used for screening in the SSTp and ISTp arms, which they considered less accurate than microscopy. Providers had reservations about giving anti-malarials presumptively as IPTp, due to concerns of causing potential harm to mother and baby and as a possible driver of drug resistance. Pregnant women were accepting of all three interventions. Women in the IPTp arm were happy to take anti-malarials presumptively to protect themselves and their babies against malaria. CONCLUSIONS: The findings indicate that, within a trial context, malaria screening of pregnant women at every ANC visit ISTp was an acceptable strategy among both health providers and pregnant women owing to an existing culture of screening and treatment. The adoption of IPTp however would require a considerable shift in health provider attitudes and a clear communication strategy. By contrast, pregnant women welcomed the opportunity to prevent malaria infections during pregnancy.