Relevant literature has emphasized the lack of a “tool orchestration” framework in e-collaboration environments (either for work or learning purposes). In this chapter, the MAPIS3 software architecture is suggested as a flexible solution to manage the key problem in tool orchestration, which is the efficient data transfer among various tools used in e-collaboration activities. The proposal is assessed by two case studies of flexible e-collaboration scenarios that cannot be implemented automatically with any known architectures or tools. These scenarios entail transfer and transformation of students' collaboration data through an IMS-LD compatible “player.” The data emerge originally to a specific tool and are transferred to another tool. The overall implementations were evaluated from the developers', the instructors', and the students' perspectives. Results indicate that MAPIS3 supports seamless data flow among tools efficiently and flexibly. In particular, teachers are supported in monitoring the e-collaboration process by flexible visualizations of peer/student interactions.