Background: Malaria in pregnancy (MiP) is an important public health problem across sub Saharan Africa. Regular use of Long-Lasting Insecticide treated bed Nets (LLINs), directly observed administration (DOT) of intermittent preventive treatment with sulphadoxine-pyrimethamine (IPTp-SP) and prompt and effective case management of MiP has constituted the package of measures for its control in Ghana in the last 20 years. 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% use of LLINs by 2015. Methods: This ethnographic study explored how managers dealt with existing MiP policy implementation and arrangement challenges and the consequences on clients’ access to MiP interventions, using observations with conversations, in-depth interviews and case studies in eight health facilities and twelve communities for twelve months, in two Administrative regions in Ghana. The University of Health and Allied Sciences’ Research Ethics Committee approved the study [UHAS-REC/A.I Ul 17-18]. Results: 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 drugs and relaxing the DOTs policy. This ensured that facilities had funds to pay creditors, purchase drugs and supplies in order to ensure continued service delivery. Clients who could afford the cost of maternal and MiP services and those who had previously benefitted from such services were happy to access uninterrupted services. Whilst clients who could not afford the cost of services resorted to health care shopping, delaying in starting ANC and skipping scheduled ANC visits. Consequently, some clients did not receive the recommended five+ doses of SP, others did not obtain LLINs early and some did not obtain recommended treatment for MiP. Frontline workers felt frustrated and demotivated, because sometimes they could not provide comprehensive care to clients who could not afford it. Conclusion: For Ghana to achieve her goal of controlling MiP, the Ministry of Health and other supporting institutions need to ensure prompt reimbursement of funds, the supply of programme drugs and medical supplies to public, faith based and private health facilities.