In 2014, Nigeria shifted its malaria policy and strategy from control to elimination. Studies show that data-driven decision making is essential to achieving elimination. It is therefore important that policy makers have access to and use good quality and relevant data to inform program decisions. This article presents findings from an assessment of availability, quality, and use of malaria data in three states in Nigeria, namely, Akwa-Ibom, Cross River, and Niger, as part of a larger study on how organizational structure affects outcomes of malaria programs. A literature search to determine the availability and range of malaria data in Nigeria was conducted, followed by 65 key informant interviews to understand how malaria data are used in the study states. It was observed that the District Health Information System (DHIS) was the major source of data used in managing programs; however, the range of malaria indicators in the DHIS is limited, lacking indicators such as active case detection and entomological data, which are important for surveillance and decision making toward malaria elimination. On data quality, routine data from the DHIS were reviewed using the national protocol for data quality assessment. Data quality was found to be suboptimal, with quality scores ranging from 54% to 64% compared to the national target of 80%. DHIS data were reportedly used most often for performance and/or supply chain management. Overall, the study demonstrates gaps in data availability and quality and highlights the need for more data sources and improved quality data to inform decision making toward malaria elimination in Nigeria.