New business condition and current economical situation are forcing companies to rethink their way of operating. The rapidity of managing changes has become increasingly important. To be more competitive, companies are forming Virtual Organizations (VO) where short-term spontaneous collaboration activities are rather common. Such interoperability leads to increasing organizational architectural complexity. As the VO interoperability availability depends on quality of companies Enterprise Architecture approach belonging to ecosystem, the current article propose focus points for architecture management in VO.