Club owner Ryan Reynolds collected his awards while dressed as Deadpool, but he and Rob McElhenney weren't present at the prize giving ceremony in Los Angeles.
The FX hit documentary took home wins in directing, editing, sound mixing and cinematography as season two of the show covered the club's long-awaited return to the Football League.
Accepting the award, McElhenney joked that he'd been 'waiting for this moment for 16 years' as his long-running cult show It's Always Sunny in Philadelphia has never been nominated.
But just as he said "I've got a lot to say…" along came Deadpool to cut him off.
"Mr Lively couldn't be here to accept this broken Emmy," he said. "So he sent me on his behalf.
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"First and foremost, Wrexham, we love you. Thanks for letting Rob and the other guy tell your story. Cymru am byth, b****es
"I'd also like to thank the academy for this honour and for not asking for us to attend the televised awards show with the real celebrities. I'd also like to thank FX for their support and in exchange Mr Lively promised not to f*** up my next movie.
"Lastly the Oscars, you're on notice motherf*****s, maybe we can get a token VFX nod next year. The amount of work on Hugh [Jackman] and Ryan's faces alone is at least worth a nod."
Reynolds was understandably raising the anticipation for Deadpool 3, his biggest movie franchise to date, which is set for release in July when Jackman will reprise his role as Wolverine.
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Welcome to Wrexham, meanwhile, will also undoubtedly be back for a third run, given the entertainment on pitch.
The Welsh side made it up to League Two after 15 years of trying last season, and could well seal back-to-back promotions as they challenge at the top of the division.
Wrexham ace Elliott Lee brutally calls out Shrewsbury player Tom Flanagan for semi-pro dig after FA Cup win
Outside of that, Phil Parkinson's team are also excelling in the FA Cup, winning their third match of the campaign against local rivals Shrewsbury.
Tom O'Connor scored the winner in a 1-0 victory, but top scorer Lee took the headlines post match.
Ahead of the match, Shrews star Tom Flanagan commented that Wrexham's players 'were semi-professional last season' and that it was 'like we've drawn a Premier League team' due to the fanfare.
Elliot made sure those comments came back to bite him post-match, saying: "It was a great performance and I'd like to dedicate that to one of their players, Tom Flanagan, who said that we were full of semi-pro players last year. So that one's for you, mate."