"The decision to be open about my sexuality and tell the world we were going to become parents absolutely petrified me," Stoney, 32, tells HuffPost UK Parents.
"Because you never know what sort of reaction you're going to get."
Stoney, who plays for Arsenal Ladies and England Women, was pleased to find the majority of the messages she received were positive, although she did get the “odd negative one”, including a letter warning her about the "health hazards of homosexuality".
"It makes you sad to realise there is still homophobia in the world," she says.
"But to anybody who ever questions why we've had children, I'd say: Well look at what we've been through to have them and look at how wanted they are."
Harris gave birth to twins Teddy and Tilly on Sunday 9 November via emergency caesarean after four days in labour.
"It was not an easy pregnancy from start to finish," says Stoney.
The couple went through three rounds of IVF before former Lincoln Ladies player Harris, 29, became pregnant.
"No one can quite prepare you for the journey you go on when you're trying to conceive," says Stoney.
"It's an absolute emotional rollercoaster."
It causes prolonged and repeated nausea and vomiting, fatigue and low blood pressure.
"Megs isn't a moaner, she didn’t moan once, but she was so ill she lost two stone when she was 16 weeks pregnant," says Stoney.
"I was so worried about her that I said enough is enough and took her to the walk in centre. They sent her straight to A&E and she sat there and cried her eyes out. I just felt so sorry for her.
"When people say that hyperemesis is just morning sickness, that's absolute garbage. It's an unbearable condition.
"They kept Megs in for four days and put her on a drip to get a bit of goodness back into her.
"Megs looked at me at one point and said 'I'm never doing this again'. I think she's changed her mind now. She'd do it all again in a heartbeat.
"We had read about Kate suffering from the same thing and it was something we referred to: 'Oh Megs has got what the princess has got.' Megs always wanted to be a princess so…"
Stoney and Harris had planned to announce the pregnancy to their families by giving them jigsaw puzzles made from their scan pictures.
However, Harris's condition meant they were forced to reveal the news earlier than expected.
"I had to go away on international duty while Megs was in hospital," explains Stoney.
"At that point we hadn't yet told anybody about the pregnancy, but I had to tell Meg's mum and dad so they could come and look after her.
"When we broke the news they said they'd had a sneaky feeling. They were over the moon to become grandparents and my parents felt the same, it was a really nice conversation to have.
"We gave the jigsaw puzzles to our siblings. We handed over the puzzles to my brother and his wife, and Meg's twin sisters and her brother, and then let them work it out for themselves."
Despite Harris's difficult pregnancy, Stoney says watching her partner give birth has made her want to experience pregnancy herself.
"I was in the theatre when they took Megs in for the c-section," she says. "It was amazing.
"Megs was convinced she was having two girls and I was convinced she was having a boy and a girl, so for the first time ever I was right and she was wrong.
"Teddy came out first, then Tilly came out about 50 seconds later.
"The way I felt when I held them for the first time is actually indescribable, because you fall in love in a completely new way.
"Every time I hold them I just feel like the proudest person in the world, but I'm sure every parent feels like that.
"The miracle of being pregnant and giving birth is such an amazing thing that I would love to do one day when I'm not playing… and when the twins are a bit older – we're not that stupid as to have three under two!”
Stoney is pleased she and Harris made the decision to be open about the struggles they faced to become parents.
“We've heard from a lot of people who really appreciate that we shared not just the fact that we were having children, but our journey through it as well,” she says.
“Because so many people, in all types of relationships, struggle to conceive and knowing you're not alone makes it easier to cope with."
Teddy and Tilly are now six months old and Stoney is settling into life as a mum.
"Being a mum is amazing, exhausting but amazing," she says.
"Having two is tougher than I expected, as you just never ever have a spare set of hands.
"But every single morning when I look in their little cots and see them asleep I feel blessed. They've completed my life."
For the time being Stoney is content with having mastered the best technique to soothe her babies when they're crying (singing Incy Wincy Spider), but she's looking forward to being able to kick a ball around with them both when they're older.
"I want to give my girl and boy as many opportunities to be physically active as they can, in any sport they like," she says. "If they happen to like football, fantastic.
"I think it's so good now that my little girl can grow up and see football as a career if she wants to. That wasn't possible when I was younger, so it just shows you how progressive the game is now."
And it's not just the world of football that Stoney feels is changing for the better.
"I did have a lot of fear about being so public with our lives, but thankfully I think the world is massively changing for the better. I don’t think I could have done what I've done five years ago.
"When my children are older, I'd like to live in a world of acceptance, where difference is celebrated.
"We're all different people, we're born with different coloured skin, we're different genders, different sexualities and have different cultures and religions. Lets just accept each other and be happy."
Stoney is sitting on the judging panel for the McDonald's Football Mum of the Year Award, which will recognise a "deserving football mum" who goes beyond the call of duty so children can experience the joy of playing football, week-in week-out.
"I wanted to be involved as obviously I've just become a mum and when I was growing up my mum sacrificed a lot to support me," Stoney says. "She worked three jobs to fund me being able to play.
"I think mums do a lot of the unsung hero work and I think it's fantastic to be able to celebrate that."
Nominations for the McDonald's Football Mum of the Year Award are now open and will close on 19 June 2015. Coleen Rooney will present the winner with their award at a ceremony at Wembley Stadium on Sunday, 2 August.