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The design and implementation of collaborative business processes and the Business-to-Business (B2B) systems that support them is an important issue in order to enable enterprises to set up B2B collaborations. This involves new challenges, mainly regarding the ability to cope with change, decentralized management, peer-to-peer interactions, preservation of enterprise autonomy, and the support for interoperability. The design and implementation of B2B collaborations require the use of conceptual models that differ in viewpoint, target people, abstraction level and granularity. This makes the use of traditional software development methodologies inappropriate. In this paper, we propose a methodology for the design and implementation of B2B collaborations that support the above issues. The methodology supports a development framework and is based on the Model-Driven Development (MDD). The methodology provides guidelines, languages, methods, model transformations and tools to support the representation of business requirements, the definition of technology-independent collaborative process models, the derivation of technology-independent processes and IT architectures that enterprises require to support collaborative processes as well as the generation of a technology-specific solution for each enterprise. This methodology guarantees the alignment and consistency between the business and technological solutions for B2B collaborations.