The Spaniard breached the governing body's kit and advertising regulations by donning a yellow ribbon as a symbol of support for imprisoned politicians in his native Catalonia.
The Manchester City manager began wearing his ribbon after Jordi Sanchez and Jordi Cuixart were placed in custody as part of the crackdown that followed last October's referendum on Catalan independence - a poll the national government in Madrid deemed to be illegal.
The legality of the ribbon in English football became questionable, as Jose Mourinho asked in a press conference in December whether such a political message should be allowed.
Guardiola was not present but his family were on board and he confirmed the widely circulated version of events at a news conference to preview City's EFL Cup final clash with Arsenal at Wembley on Sunday.
Since October he has sought to bring attention to the plight of jailed pro-independence politicians Jordi Sanchez and Jordi Cuixart by wearing a yellow ribbon at during all City matches and media engagements.
The City manager was born in Santpedor in central Catalonia and was manager of Catalan club Barcelona before joining the Premier League side.
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"If they want to suspend me - UEFA, Premier League, FIFA - it's OK".
Guardiola has been a vocal proponent of Catalan independence and the FA charge was the second time on Friday his political alignment placed him in the headlines.
Despite the massive pay boost, Guardiola is still yet to get his hands on a trophy at City - and recently saw his quadruple hopes crushed by Wigan in the FA Cup.
"To make a rebellion on something like that, you have to be something tough to be in prison".
"Like everybody knows, hopefully sooner or later I can stop wearing it (the ribbon)".
Pep Guardiola hasn't only been in the news due to the FA.