The comedy creator picked up the awards for Outstanding Lead Actress In A Comedy Series, Outstanding Comedy Series and Outstanding Writing For A Comedy Series.
Referencing her character in the sitcom, she said: "It's so wonderful and reassuring to know that a dirty, pervy, angry and messed-up woman can make it to the Emmys."
She jokingly added, whilst holding up the trophy: "I find writing really hard and really painful, but I'd like to say from the bottom of my heart that the reason that I do it is this. So it's made it all really worth it guys, thank you so much."
Additionally, the BBC Three comedy's director, Harry Bradbeer, won the Outstanding Directing For A Comedy Series title. He said: "For a director, something like Fleabag only comes along once in your life. Thank you Phoebe for coming into my life like some kind of glorious grenade. Scientists are still trying to work out how someone so incredibly talented can be so utterly lovely."
On picking up the comedy series award, Waller-Bridge commented: "This is getting ridiculous! Fleabag started as a one-woman show at the Edinburgh festival in 2014, and the journey has been absolutely mental to get here."
Paying tribute to the "hot priest" character, she added: "Season 2 would not have exploded in the way that it did if it wasn't for Andrew Scott, who came into our Fleabag world like a whirlwind and gave a performance of such depth and complexity it elevated the whole thing."
Fleabag is available through [z]Amazon] in the US, making it eligible for the country's prestigious Emmy Awards.
Here is a video of the star talking to the press back stage:
Elsewhere in the ceremony, Charlie Brooker was amongst the team who picked up the award for Outstanding Television Movie, for the video game-linked Black Mirror episode Bandersnatch. Thanking his two children, he joked: "I can never limit your video game screen time again, if I do I'm a disgusting hypocrite - it sometimes pays off."
Other British winners at the Los Angeles ceremony included Killing Eve star Jodie Comer (Leading Drama Actress), Ben Whishaw (Supporting Actor In A Limited Series, for A Very English Scandal), John Oliver (Outstanding Variety Talk Series) and Jesse Armstrong (Writing For A Drama Series, for Succession). The Peep Show co-creator jokingly commented: "Quite a lot of British winners; maybe too many? Maybe you should have a think about those immigration restrictions!"
Game Of Thrones won many awards at the ceremony too. Full results can be seen on emmys.com
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