After leaving an assistant manager role at Wolfsburg to head to England, he oversaw the transformation of Arsenal’s youth system while in north London - with the Hale End academy undergoing a complete rebuild.
Arsenal are, however, prepared to acknowledge that the opportunity to take a first-team post in Germany was too good to turn down.
Chief executive Ivan Gazidis told the club’s official website: "This is a great opportunity for Andries and we wish him every future success. Under Andries' guidance, we have made huge progress in our academy operations.
“Arsenal is known around the world for its development of young players and we are confident we will find the right person to continue to lead our progress."
Commenting on his move, Andries said: "I have had a wonderful three years at Arsenal. We have made significant progress and it has been great to be part of a club which puts such an emphasis on developing young players through its academy.
“I leave a great team of people who will continue to do a terrific job and I would like to thank everyone, including the board, chief executive Ivan Gazidis and Arsène Wenger for all the support.
“There are some top young players in the Arsenal academy. I look forward to seeing them progress their careers."
Jonker has penned a deal with Wolfsburg through to 2018 and has been welcomed to the club by sporting director Olaf Rebbe.
He told his team's official website: "Andries Jonker knows VfL Wolfsburg well and maintained regular contact with the club even after his move to London. Both factors were vital in us achieving this top solution so quickly.
"He is an internationally experienced coach and an expert tactician, who provides the best possible requirements to get VfL back on track quickly and sustainably."