"Peter Beardsley has been charged with three breaches of FA Rule E3," the FA said in a statement.
"It is alleged Mr Beardsley used abusive and/or insulting words towards Newcastle United FC Under 23 players, which were contrary to FA Rule E3(1), whilst employed as their coach.
"It is further alleged these words also constituted an 'aggravated breach', which is defined in FA Rule E3(2), as they included reference to ethnic origin and/or colour and/or race and/or nationality."
The club launched an investigation into the allegations last year but did not publish a report on its findings.
Beardsley, who spent the majority of his playing career at Newcastle, denied the accusations of bullying at the time and again at a public-speaking event in Gateshead last weekend.
"I'm not a bully, and I'm not a racist," Beardsley told reporters.
"Everybody in the city of Newcastle has been amazing, for 15 months, they've been amazing. I know what I am and everybody who knows me, my family, my friends, knows what I am.
"I'm comfortable with what I am. It is what it is, I'm just ready to move on."
Beardsley has until April 12 to respond to the charge.
(Reporting by Rohith Nair in Bengaluru; Editing by David Goodman and Christian Radnedge)
