A majority of today’s cloud services are independently operated by individual cloud service providers. In this approach, the locations of cloud resources are strictly constrained by the distribution of cloud service providers’ sites. As the popularity and scale of cloud services increase, we believe this traditional paradigm is about to change toward further federated services, a.k.a., multi-cloud, due to the improved performance, reduced cost of compute, storage and network resources, as well as increased user demands. In this paper, we present COMET, a lightweight, distributed storage system for managing metadata on large scale, federated cloud infrastructure providers, end users, and their applications (e.g. HTCondor Cluster or Hadoop Cluster). We showcase use case from NSF’s, Chameleon, ExoGENI and JetStream research cloud testbeds to show the effectiveness of COMET design and deployment.