The COVID-19 pandemic has urged higher education institutions (HEIs) to improve their information technology (IT) capabilities due to online demands in almost all activities. However, a large IT investment does not guarantee added value for an organisation if the effectiveness of IT governance does not accompany it. Since studies on this issue are still lacking, this study examined the effect of IT capabilities and perceived effectiveness of IT governance on the accountability and performance of HEIs during the COVID-19 pandemic. This study also tested the role of IT governance as a mediator. This study employed a survey method with hypothesis testing using the Partial Least Squares (PLS) technique. The sample comprised 129 HEIs located on Java Island, Indonesia. Cluster sampling was utilised to ensure the representativeness of the sample between the provinces located in Java, covering Banten, the Special Capital Region of Jakarta, West Java, Central Java, East Java, and the Special Region of Yogyakarta. The results showed that when IT capabilities positively affected IT governance, either IT capabilities or IT governance positively affected HEIs accountability and performance during the COVID-19 pandemic. Further, IT governance was found to be a mediating variable.