Arsenal head of football Raul Sanllehi is leaving the London side and will be replaced with Vinai Venkatesham, the club announced on Saturday.
Sanllehi joined Arsenal from Barcelona in 2018, initially acting as the club's head of football relations.
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"Raul has made a big contribution during his time with us and will always be part of the Arsenal family. We thank him for all his hard work and expertise and wish him every future success," owners Stan and Josh Kroenke said in a statement.
"We have no doubt that Vinai is the right person to take the club forward. He has shown outstanding leadership during the current crisis and is held in high regard internally and externally. We know everyone will rally round him so we can move forward successfully."
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Venkatesham has been at the club since 2010 and replaced Ivan Gazidis as managing director.
"There is much work to do to return Arsenal to the top of the game where we belong, which is what our fans rightly demand. While this will not happen overnight, I believe we have many of the critical ingredients to do so. There are many positives to build on across the club," he said.
"While football faces uncertainties ahead as a result of the COVID-19 pandemic, I am confident Arsenal will emerge strongly and look forward with confidence."
There had been growing discontent at the way transfers were being run at the club, with an investigation launched into whether Arsenal overpaid when they bought Nicholas Pepe for €72 million.
In July, Arsenal also announced 55 non-playing staff redundancies as the financial concerns over the coronavirus pandemic mounted.