The 34-year-old fitness coach, TV presenter and author, took to his Instagram page today to announce the news.
The star, who is also known as The Body Coach, shared a snap of himself in his sportswear as he held CiN mascot Pudsey Bear on his shoulders.
He told his 3.9million followers: "All money raised from @YouTube ads for PE With Joe will be donated to BBC Children In Need.
"As an ambassador this is a charity that is close to my heart and all the money raised will be going on to support local charities and projects including those which focus on mental wellbeing, loneliness and isolation or support families facing poverty and deprivation caused by the pandemic."
The post instantly began racking up thousands of likes as Joe was labelled a "hero".
One fan told him: "You are one of our heroes Joe, thank you."
While another added: "Well done Joe, true legend."
A third chimed in: "What a great bloke you are Joe."
While the official CiN Instagram account replied: "Thank you Joe," alongside a yellow love heart.
The fitness guru started the PE With Joe videos back in March last year in response to the coronavirus pandemic and the UK lockdown.
After it was announced that all schools would be closed and we'd all be spending more time at home, Joe decided to share free workout video to keep the nation, especially children, moving as well as healthy and positive.
The BBC has also announced today that it plans to keep the nation fit through lockdown with help from stars from the world of sport and entertainment, including Joe, in a series of programmes.
Strictly Come Dancing stars, Mark Wright, Mr Motivator, Kevin Sinfield, Adam Peaty, Tyrone Mings and others will also take part.
Kicking things off on January 11 is BBC Breakfast: Lockdown Life. This segment will see stars provide top tips to keep both the body and the mind active for viewers of all ages.
Joe will start the series at 7.50am on BBC One followed throughout the week by Mr Motivator, rugby league legend Kevin Sinfield, Olympian Adam Peaty and Premier League footballer Tyrone Mings for the rest of the week.
CBeebies’ Maddie Moate and partner Greg Foot will also join BBC Breakfast regularly to offer advice for home schooling and fun activities to try.
Joe has also been hitting headlines this week as it was announced he is one of the top earning fitness influencers around right now, according to a new fitness influencer rich list.
According to the list, Joe earns an average monthly salary of £341,660 and £7,927 from each of his social media posts to his 3.8million followers.