The Gunners have paid the O's a compensation fee for Beckford determined by the Elite Player Performance Programme compensation agreement, reports the Daily Star.
Leyton Orient Academy director Andy Edwards said: "He has been a credit to the club all the time he has been here.
"We are disappointed to lose him. We wish him all the best at Arsenal.
"We have got some exceptional players in our academy of which Jay is one.
"Arsenal have met the valuation which is linked to the EPPP guidelines and unfortunately we lose him."
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