Nowadays, higher education institutions generate vast amounts of data integrated from diverse data sources, ranging from academic information to research achievements. These data are gathered from several systems implemented at each higher education institution in Malaysia. These data are often heterogeneous in nature and have different formats and structures. Hence, the data should be integrated into a central warehouse to perform a holistic analysis. Currently, data about students and graduates are stored in two different warehouses, referred to in this article as WarehouseA and WarehouseB. Unfortunately, heterogeneity poses significant challenges to data integration efforts that require extensive data checking and preprocessing to ensure data quality. Since these warehouses contain some similar attributes to students’ profiles, the integration of these warehouses is necessary to reduce the challenges. However, the integration of these warehouses still introduces some quality issues. Therefore, this exploratory study was carried out to investigate the challenges of data integration of higher education data in Malaysia using an action research approach. Findings from the investigation highlighted the data quality issues faced during the integration process and outlined suggestions to address these issues. This contribution is pivotal for improving data governance frameworks to ensure the quality of integrated data for higher education institutions.