The BBC One show was named Best Soap at the ceremony, with Gillian Wright, who plays Jean Slater, picking up Best Actress.
Earlier this year, programme bosses were forced to defend a storyline in which bipolar disorder sufferer Jean was being treated cruelly, following complaints from viewers.
Hetti Bywater won Best Newcomer for her portrayal of Albert Square's Lucy Beale, while comic actors Tameka Empson and Ricky Norwood, who play Kim Fox and Arthur 'Fat Boy' Chubb, were voted Funniest Female and Funniest Male.
The Best B***h crown was awarded to Charlie Brooks, who plays scheming Janine Butcher and is taking a six-month break from EastEnders.
David Witts, who joined the show this year as Derek Branning's estranged son Joey, was named Sexiest Male.
Meanwhile, Hollyoaks actor Emmett Scanlan was celebrating a double success at the awards.
The Irish star won Best Actor and Best Bad Boy for his performance as villain Brendan Brady.
Coronation Street favourite Michelle Keegan was named Sexiest Female for the fourth year in a row.
Although she was unable to attend the ceremony, Michelle was thrilled with her double-scoop at the show.
She tweeted: "Thankyou sooooo much to everyone who voted for me at The Inside Soap Awards. I'm over the moon with the awards! The fact that people have gone out of their way to vote is unbelievable, I'm so grateful! Sorry I can't be there to pick them up. You've made a girl very happy! Xx
She was also named the Best Dressed Soap Star, held at the plush One Marylebone in London.
Fellow Corrie star Alex Bain, who plays Simon Barlow, was named Best Young Actor.
Australian soap Neighbours received two awards, Best Daytime Soap and Best Daytime Star for Ryan Moloney, who plays show stalwart Toadie Rebecchi.
BBC One show Waterloo Road picked up its third Best Drama award.
Inside Soap editor Steven Murphy said: "It's been an exciting year in the world of soap... We can't wait to see what the next 12 months have in store for our great British soaps."