Toon youngster Yasin Ben El-Mhanni lodged a complaint against Beardsley regarding alleged racist comments, leading to a probe being launched on Monday.
Following a meeting with managing director Lee Charnley and head of safeguarding Steve Swinyard, a decision has now been taken for the legendary Newcastle and England striker to spend some time away from St James' Park.
A club statement read: "After discussions with Peter Beardsley this morning it has been agreed that he will take a period of leave, to commence immediately, whilst the club conducts its investigation into allegations made against him.
"It would be inappropriate for the club to comment further until the conclusion of this investigation."
According to The Sun, one of the alleged incidents took place during a trip to Go Ape adventure course when, with two African players struggling on a climbing frame, the 56-year-old quipped: "Why are you taking so long? Your lot should be good at this."
United are expected to speak to a number of academy players before making a final decision on Beardsley's future.