In 2015, the historic church received a £1.5m donation and Heritage Lottery Fund money for a restoration project which included creating eco-friendly under-floor heating and repairing the collapsing floor.
Included in these plans was the controversial move to get rid of the pews to make it a more flexible space.
After nearly 10 years of planning, the Chancellor of the Diocese of Bath and Wells has granted them permission.
In a statement on the church website, Rev Edward Mason of Bath Abbey said: "We are delighted with the decision of the Consistory Court.
"We strongly believe in the benefits of removing the pews.
"It will enable us to open up the Abbey's nave and side aisles to all and make it possible for people of different physical ability to sit where they choose.
"Stackable chairs mean that the nave can be used for a wide variety of traditional and contemporary worship and restore the Abbey to the community use for which it was first designed."
The Victorian Society opposed the desire to remove the pews because of the "detrimental effect on the architectural and historical significance of this important religious building", according to their online petition.
