Research on organisational arrangements of scholarly networks in both e-learning and e-research is located at the intersection of different theoretical justifications and developmental contexts such as organisational theory, computer science, education science and media informatics. However, there is still a lack of research on the organisational context of e-learning arrangements and its impact on collaboration in academic communities. E-learning research shows that the integration of electronic media in scientific communities negatively impacts their effectiveness and causes conflicts within communities. Research networks however are far less investigated as there is not direct didactic focus on how to collaborate. Recent theories on organisational design, virtual organisations and governance provide concepts for organising e-collaboration more effectively. Managerial instruments such as direct control of results and behaviours need to be supplemented or even replaced by concepts of social control; typically trust and confidence become the central mechanisms for the new forms of inter- and intra-organisational coordination. This paper starts with concepts. Then, to exemplify the organisational coordination mechanisms in scholarly e-communities, the authors critically discuss and reflect on these organisational arrangements and managerial concepts for two higher education portals and one research network in Germany. The conclusion is that, just as previous research has confirmed for educational networks, governance within academic networks relies heavily on the functionality of social and communicative forms of control.