A representative for the Sicario star confirmed that Emily is pregnant again, after she and John welcomed their daughter Hazel in February 2014.
The private couple rarely opens up about their personal lives, preferring to let their impressive body of work do the talking.
But both have shared snippets on how much parenthood has changed them since Hazel’s arrival.
Emily, who is currently filming The Girl On The Train alongside Justin Theroux and Lisa Kudrow, told Radio Times magazine in 2015 how motherhood has affected her.
“It changes you infinitely in a rather overwhelming way,” the 32-year-old says.
“You don’t know what to expect because it’s just completely, existentially out of anything that you’ve ever experienced before, and it’s quite indescribable.
“The best way I can describe it is that it’s like this lovely distraction that I always have.
“It’s always there and I love that feeling.”
John has earlier admitted to People magazine that he experienced an “existential crisis” following Hazel’s birth.
“I went through some really serious stuff,” explains John, 36, who is best known for his role on the US version of The Office.
“There is a mirror that is held up to me now. You have someone watching you. You have to lead by example.”
But judging by a recent chat with Ellen DeGeneres, John has clearly relaxed into the role.
“She’s talking a lot,” he says of Hazel. “[Instead of saying] Where’s Daddy? she asks, ‘Where is that Daddy?’”
“She’s starting to do little bits, which is hilarious. She’s also picking up on Emily’s (English) accent.”
Emily and John started dating in 2008 and got married two years later in 2010 at George Clooney’s villa on Lake Como, Italy.
John and George are longtime friends and are often spotted out in Hollywood enjoying double dates.