The presenter, 41, shared his news during Wednesday’s episode of the BBC One programme.
Becoming emotional, he explained: “I’ve loved that The One Show has been such a big part of my life for the last nine years.
“It’s been brilliant to showcase the eclectic mix of Britain, meet incredible people along the way and witness so many lives changed with the annual Rickshaw Challenge for Children In Need.”
“I’d like to thank all those I’ve worked with over the years and especially you the viewer for showing me so much support during my time on the green sofa," he continued.
“I’m continuing with Countryfile and BBC Sport and excited about other opportunities that come my way but most of all I’m looking forward to having dinner with my family and being able to put my kids to bed.”
Bakerr will step down in spring 2020 which means bosses have over six months to find a replacement.
But who could possibly fill his shoes? Here are 7 stars who would be perfect for the job...
Angelica Bell, who was seated besides her co-host Baker as he delivered his teary announcement, would make a fantastic permanent presenter.
Bell often sits in for Alex Jones and also co-presents The Martin Lewis Money Show.
TV viewers may also remember Bell from her CBBC days and she also previously won Celebrity MasterChef.
With 12 years of presenting experience as a reporter and guest presenter, Bell would be the perfect permanent addition.
One of the busiest people in British television, the 31-year-old first rose to fame after finishing in fifth place in the ninth series of The X Factor and later won Celebrity Big Brother.
After triumphing on the show, he presented spin-off Big Brother's Bit on the Side, landed a guest hosting job on This Morning and returned to where it all began, with a stint on The Xtra Factor.
Clark-Neal is currently the host of the Supermarket Sweep revival and will also host a new series of Ready Steady Cook in 2020.
He's also doing a stunning job of sharing It Takes Two presenting duties with Zoe Ball so we know he can keep the tea-time audience engaged.
Yes, his schedule is packed. But it's for a good reason. Surely he could squeeze one more programme in?
After fast becoming one of our favourite Gogglebox stars, Moffatt won the sixteenth series of I'm a Celebrity...Get Me Out of Here! in 2016 and went on to present spin-off show Extra Camp for two years.
She also appeared Ant & Dec’s Saturday Night Takeaway but it was recently announced that she won't be back for the next series - so has plenty of time to take on this.
Amfo currently hosts the mid-morning show – which includes the famous Live Lounge - on BBC Radio 1 and regularly presents backstage at the Brit Awards.
She's no stranger to our TV screens either and presents Top of the Pops as well as segments of the BBC's Glastonbury coverage.
Her popularity with younger audiences could be a huge selling point as she could bring new viewers to the magazine show.
James fronts the Radio 1 Breakfast Show and co-presents the TV show Sounds Like Friday Night.
In 2011, James began presenting the BBC Three's coverage of Glastonbury and in August 2012, the Reading and Leeds Festival (both with Fearne Cotton).
In November 2016, James co-presented the BBC's Children in Need appeal for the first time and proved his versatility when he presented BT Sport's cricket coverage of the South Africa tour to Australia in 2016 and 2017.
The professional dancer is no stranger to live television.
She is best known for her time on Strictly Come Dancing and earlier this year, she wowed fans when she moved to the other side of the judging panel on The Greatest Dancer.
The 29-year-old is well-known for her bubbly personality and she's even had a test run on The One Show, when she stepped in to present two episodes earlier this year.
If Mabuse doesn't get the job then perhaps one of her fellow Strictly 2019 stars will.
Zeroual has won over plenty of new fans on the current series of Strictly Come Dancing contestant but he's no stranger to high pressure TV jobs.
The fresh-faced 26-year-old has years of experience from CBBC and has also worked on Wimbledon Live and Midlands Today.
The One Show airs on weeknights at 7pm on BBC One.