Edu will serve a six-month period of gardening leave with assistant sporting director Jason Ayto stepping into the breach while Arsenal scout for a successor.
Arsenal are prepared to wait for the right person as a long-term replacement for Edu rather than rushing to make an appointment.
A key component for Arsenal is finding someone who dovetails and works well in partnership with Mikel Arteta; the effectiveness of that relationship is felt to be linked to how strong Arsenal can be.
While losing a sporting director mid-season and somewhat abruptly is not ideal, the club are calm about the situation. There is a feeling Edu that has installed a solid structure, with the ownership having shown a skill for hiring accomplished people in all key departments.
The overriding feeling towards Edu's decision has been one of gratitude and well wishes for the work that the Brazilian has done.
During the international break, the football leadership team will meet with owners the Kroenke family to discuss strategy and squad-building ahead of the next windows. The gathering is a tradition, and Edu's successor will be on the agenda.
While Arsenal have been understanding of Edu's decision to depart for a wider remit, some staff are stunned by his choice of new role, despite his known friendship with Evangelos Marinakis.
Part of the appeal for Marinakis is that he respects the way Edu conducts himself. Edu's excellent reputation - amongst peers, agents, players and managers - is also seen as pivotal to growing Marinakis' stable of clubs.
Marinakis understands the value of Edu's expertise and esteem, and Sky Sports News understands the kind of figure being mooted as a potential salary would leave Pep Guardiola, Arteta and Unai Emery as the only managers earning more than Edu.
Edu enjoys being challenged and he feels the scope of this role, which is effectively the role of Group CEO role, will test him in new ways.
There is also a belief that his hardest work at Arsenal is already done in terms of changing the culture, building healthy structures and an environment of excellence. There is also the feeling that Edu has helped turn Arsenal from a punchline to title challengers, putting all the tools in place for the club to make the final step.