In this paper, we address several critical security issues that bottle up the wide adoption of the Cloud Computing technology. In the last years the Cloud Security Alliance (CSA) has identified many security issues that should be considered during the design of Cloud systems. We experienced them developing the Security-Enhanced (SE) CLEVER, the secure release of CLEVER, a Message Oriented Middleware for Cloud computing based on the well-known XMPP protocol. SE CLEVER provides a secure inter-module and inter-Cloud communication system useful for managing Federated environments. The secure communication system of SE CLEVER was designed leveraging the XMPP flexibility. The experimental results show how the secure capabilities introduced in SE CLEVER do not affect the overall performances of the middleware.