As corporations rely more on collaboration with partners to enhance their position in the business world, they transcend their traditional information system boundaries. They use IT-based inter-organizational information systems (B2B systems - Business to Business) as a powerful strategic tool to link with their partners in their supply chain. The B2B systems are critical for businesses in the current intensive and competitive market. By considering the concepts of inter-organizational business process (IOBP), this paper proposes an MDA-based methodology for B2B systems development which relies on the principles of BPM (Business Process Management) and SOA (Service Oriented Architecture). Thus, our methodology considers three levels in a top-down manner: collaborative business (organizational), business process (conceptual) and process execution (technological). We have proposed an UML AD profile for IOBP modelling. Then, the specific partner’s processes are derived based on MDA-based model transformations. Finally, the B2B interactions are represented using Web services technology. In addition, we validate the practicability of our methodology with the implementation of an e-procurement system.