Migrating an existing application to the cloud is a complex and multi-dimensional problem requiring in many cases adapting the application in significant ways. Taking a look in particular into the database layer of the application, this involves dealing with differences in the granularity of interactions, refactoring of the application to cope with remote data sources, and addressing data confidentiality concerns. In this chapter we introduce an application migration methodology that incorporates these aspects, and a decision support, application refactoring and data migration tool which supports application developers in realizing this methodology. We evaluate the proposed methodology and enabling tool using a case study conducted in the context of an e-science project.