Federated Research Data Infrastructures aim to provide seamless access to research data along with services to facilitate the researchers in performing their data management tasks. During our research on Open Science (OS), we have built cross-disciplinary federated infrastructures for different types of (open) digital resources: Open Data (OD), Open Educational Resources (OER), and open access documents. In each case, our approach targeted only the resource “metadata”. Based on this experience, we identified some challenges that we had to overcome again and again: lack of (i) harvesters, (ii) common metadata models and (iii) metadata mapping tools. In this paper, we report on the challenges we faced in the federated infrastructure projects we were involved with. We structure the report based on the three challenges listed above.