ABSTRACT The practice of fact-checking by journalists and fact-checking practitioners has become increasingly popular due to political events occurring alongside increasing disinformation. This practice has spread from the United States to Europe, Latin America and, Asia, including in Indonesia. However, the growth of fact-checking institutions has not been accompanied by discussions about their underlying epistemology. This study builds upon critical points raised by Uscinski & Butler (2013) regarding the epistemology of fact-checking, namely the impact of selection and unclear fact-checking criteria. We employ content analysis of publicly available fact-checking articles published by seven existing Indonesian fact-checking organizations. The patterns identified in the content analysis serve as the foundation for the interpretation of the epistemological underpinnings of fact-checking practices. This analysis is further complemented by interviews with informants from all seven organizations. This study also compares the epistemological foundations of journalism-based fact-checking with Civil Society Organization (CSO)-based fact-checking in Indonesia. We found an epistemological dilemma within Indonesian fact-checking, leading to the arbitrary nature of the fact-selection process, thereby posing a potential risk of introducing bias into the fact-checking outcomes. Our hope is that this study will be useful for fact-checking practitioners and media educators to discuss the epistemological aspects of fact-checking practices.