Institutional repositories were created to collect, preserve, and make available the academic institution’s scientific output. The purpose of this study is to investigate and illustrate how Greek academic libraries with institutional repositories deal with copyright challenges. The study aims to identify and describe if institutional repository managers apply a certain copyright clearance protocol, the problems they encounter, and how they deal with them. For this study, a quantitative research method based on questionnaires was employed. The questionnaire consisted of twenty-nine (29) questions separated into three (3) sections and was sent to thirty-one (31) academic libraries. According to the survey results, the majority of academic libraries have an institutional repository and provide open access to its content. It was found that academic institutional repositories face intellectual property difficulties. The biggest issue highlighted was a lack of knowledge of the notion of copyright. Finally, communication amongst libraries seems to be the foundation for developing a common policy and addressing the difficulties that have arisen in institutional repositories as a result of Greek copyright legislation limits.