Just eight months after giving birth to their first daughter Ethel, the singer is reportedly pregnant with her second child.
The couple have yet to officially confirm the news, but after receiving various congratulations through Twitter, the star tweeted a message that seemed to give it away.
"Thank you for all your congratulations today. I honestly couldn't be happier. Such an honour to be on the list! Timestop50tweeters," she wrote.
The Daily Mirror were first to report that Lily had her three-month scan last week and has been told that all is well.
A source told the paper: "It was a surprise but Lily and Sam are thrilled.
"The pair of them have loved every minute of parenthood so far and wanted to expand their brood quickly. So it's great timing."
It will be a busy year for the star who is currently working on her comeback album, her first since taking a break from the limelight two years ago to start a family.
She has also just finished working on the score for the Bridget Jones' Diary West End musical.
The source added: "Lily’s got lots on her plate right now. She’s been working on a handful of songs already and has lots more ideas of what she wants to do.
"But like everything in her life, work comes second to Sam, Ethel and now their bump. She's just so excited."