She will be replaced on the 10am slot by Fun Lovin' Criminals star Huey Morgan from November 2.
The BBC said the presenter, from Anstruther, Fife, will continue to work with the station.
A spokesman for the BBC said: "Edith Bowman's series will come to an end but she will continue to work with 6 Music with occasional specials planned for next year."
Meanwhile, former Catatonia star Cerys Matthews has had her Sunday morning show extended by an hour.
The star, who was named music broadcaster of the year at this year's Sony Radio Academy Awards, said: "I'm happy that I can now lay down what I think will be not only a Sunday morning show to wake up and ease the listeners into their day of rest, but take it right through to provide the perfect soundtrack to their Sunday lunch."