The Scottish DJ and presenter, who presents the station's Review Show on Tuesdays, is one of several household names who will leave Radio 1 and 1Xtra on September 1. Other presenters leaving include Nihal, Mike Davis, Jen Long, Ally McCrae and Rob Da Bank.
The changes are designed to enable Radio 1 and 1Xtra to deliver some of the savings they have been asked to make by the BBC.
Ben Cooper, Controller, Radio 1 & 1Xtra, said: "These cuts to our budget are hurting, it means I have had to make some tough choices and say goodbye to some friends and respected colleagues. I believe these new schedules continue to innovate, reflect and celebrate the UK's youth and music culture."
Bowman's departure was announced as Radio 1 unveiled plans for a new rock show, which will be presented by Daniel P Carter and air after the Official Top 40, as part of a change to its specialist programming.
Other new programmes include a weekend afternoon show hosted by Alice Levine and a new music programme presented by Huw Stephens.
Radio 1Xtra also has a new look with new shows hosted by Monki, Sian Anderson, Seani B and rapper A.Dot.
Daniel P Carter said: "To be starting the show directly after the announcement of the UK number one is obviously amazing and to be in the position where my show is an alternative option to the Simon Cowell circus is also a beautiful thing. If that's your bag then all good, but I'm stoked that The Rock Show will be in a slot that reflects the importance of a genre that is now, and always will be, in great shape because it is everything to the people that love it."
Alice Levine said: "In the 18 months since I joined Radio 1 I've already had so many incredible experiences. And now to be given a weekend daytime show really is a huge privilege. Bring on September!"
Huw Stephens said: "Night-time is a special time at Radio 1, and there is a strong tradition of supporting new artists, so I am delighted to be presenting a new show that will play excellent music and champion BBC Introducing artists as we end the day together."
Sian Anderson said: "I'm overwhelmed to be given this opportunity. Having a specialist show is perfect for me - I love music and I love showcasing new talent. I'm really excited to now take it to the next level and show everyone what I can do and it's even more amazing to be joining with my St Lucian sister A. Dot."
A. Dot said: "After many years on the other side of the desk it's incredible to be able to now sit in the presenter's chair. 1Xtra has always felt like home to me so it's great to now be part of the family. I can't wait to get stuck in, The Dotty Show is gonna be unmissable!"