But here they are, nine months on, the proud parents of a baby girl and – according to Pete – stronger than ever.
In fact, Pete is so loved-up that just days before their daughter Amelia was born, he proposed to Emily.
"I can't even begin to tell you how much I love Ems," gushes the 40-year-old singer when we catch up with him in a central London hotel. "Did we plan the pregnancy? No. Was it slightly foolish? Perhaps, but the point is that I always knew Emily was the person I wanted to spend the rest of my life with."
He adds: "I wanted to be engaged before the baby was born. In fact, I'd have loved to be married before the baby was born. I'm quite traditional and by the traditions set by my mum and dad, you get married and then have kids.
"I know it doesn't always work like that, especially these days – but at least we're engaged now and Emily's my fiancée, not my girlfriend. It feels nice."
While the couple are ecstatic about the arrival of their daughter, who was born three weeks early, like any new parents, they are experiencing the joys of sleepless nights.
And unlike most celebs, Pete and medical student Emily, 24, have decided not to hire a nanny and are handling things themselves.
Pete says: "Sleep deprivation isn't great, but you can't help but be excited. I'm always asking Emily if she's okay and if everything's okay. But, if I'm honest, I do it with half-closed eyes because Emily is breastfeeding so she has to do all the feeds."
As for who their baby looks like, Pete smiles as he says: "She's a mini Ems! Her nose is mine, but the rest of her is Emily."
"But I also want her to have my creativeness and drive."
Speaking of his drive, Pete initially said he wanted a month off after the birth so he could spend time with his family. However, just three weeks later he's back at work promoting his single, Kid, from children's animated movie Mr Peabody and Sherman.
"I love working," he tells us. "But I love working for the right reasons. I want to support my family, my friends, my brothers. It's important to stick to my commitments – and I still get to spend lots of time with Emily and the baby."
Read the full interview in this week's Reveal magazine. Out now
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Peter and Emily's relationship in pictures: