This paper explores the challenges of constructing an architecture for inter-organisational collaborative interactions based on Service Oriented Architecture (SOA), Web services choreographies and software agents. We present an approach to harmonisation of the “global” or neutral definition of business collaborations, with partner-specific implementations, which can differ in terms of platform, environment, implementation technology, etc. By introducing the concept of pluggable business service handlers into our architecture we draw on the work carried out by ebXML initiative, business services interfaces, in particular. Due to increasing need for better management of collaborative interactions, Virtual Organisations (VO) become an important tool for creation and maintenance of federated trust domains among the collaboration partners. We look into the software agents abilities to serve as the background support mechanism for the automation and management of the Virtual Organisations lifecycle.