BackgroundMalaria in pregnancy (MiP) is an important public health problem across sub-Saharan Africa. The package of measures for its control in Ghana in the last 20 years include regular use of long-lasting insecticide-treated bed nets (LLINs), directly-observed administration (DOT) of intermittent preventive treatment with sulfadoxine-pyrimethamine (IPTp-SP) and prompt and effective case management of MiP. Unfortunately, Ghana like other sub-Saharan African countries did not achieve the reset Abuja targets of 100% of pregnant women having access to IPTp and 100% using LLINs by 2015.MethodsThis ethnographic study explored how healthcare managers dealt with existing MiP policy implementation challenges and the consequences on IPTp-SP uptake and access to maternal healthcare. The study collected date using non-participant observations, conversations, in-depth interviews and case studies in eight health facilities and 12 communities for 12 months in two Administrative regions in Ghana.ResultsHealthcare managers addressed frequent stock-outs of malaria programme drugs and supplies from the National Malaria Control Programme and delayed reimbursement from the NHIS, by instituting co-payment, rationing and prescribing drugs for women to buy from private pharmacies. This ensured that facilities had funds to pay creditors, purchase drugs and supplies for health service delivery. However, it affected their ability to enforce DOT and to monitor adherence to treatment. Women who could afford maternal healthcare and MiP services and those who had previously benefitted from such services were happy to access uninterrupted services. Women who could not maternal healthcare services resorted to visiting other sources of health care, delaying ANC and skipping scheduled ANC visits. Consequently, some clients did not receive the recommended 5 + doses of SP, others did not obtain LLINs early and some did not obtain treatment for MiP. Healthcare providers felt frustrated whenever they could not provide comprehensive care to women who could not afford comprehensive maternal and MiP care.ConclusionFor Ghana to achieve her goal of controlling MiP, the Ministry of Health and other supporting institutions need to ensure prompt reimbursement of funds, regular supply of programme drugs and medical supplies to public, faith-based and private health facilities.