City's Shaun Wright-Phillips, in particular, was targeted by the home crowd in England's 1-0 defeat in Mardrid on Wedensday, after replacing David Becham on the hour-mark for his third senior cap.
And on the previous evening, the Darren Bent, Carlton Cole, and Glen Johnson suffered similar treatment while playing for the U21s, when they also lost 1-0.
Now a two-page letter will be given to the world governing body, with a copy to Uefa, detailing the racist chants - which were also directed at Ashely Cole, Rio Ferdinand, and Jermaine Jenas.
The document also highlights the FA's concern at the lack of action taken regarding the inflammatory remarks that were made by Spain manager Luis Aragones.
The FA's head of media, Adrian Bevington, told the BBC the racist chants were "a disgrace" and added: "Football as a whole should stand up and express its disgust at what has gone on here."
The Spanish had said nothing to condemn the actions until early today, when their foreign minister Miguel Angel Moratinos apologised, "in the name of the Spanish government, to anyone who may have felt offended by these expressions.
"I have had the opportunity to comment and discuss it with my (British) counterpart Jack Straw and I again express that Spain is a country of tolerance where expressions of racism should have no place," added Moratinos.
As a result of the investigation, the Spanish FA could face a large fine or the national team could even be handed a five-match ban.
And as for Wright-Phillips, City's head of communications, Paul Tyrrell, reckons he'll be just fine.
"Shaun is a strong character who will be unaffected by what happened and we are sure that the football authorities will deal with the problem appropriately," he told the City website.