The key points of the treaty stipulated that:
- The Female Changeling would surrender herself to the United Federation of Planets to stand trial for war crimes.
- All Dominion military personnel were to commence a complete withdrawal from the Alpha Quadrant within 26 hours of the general cease-fire.
- All territory occupied by the Dominion would be returned to their respective sovereign powers, including the Cardassian Union and Breen Confederacy, as the agreement explicitly states all Dominion territory, including by treaty, must be ceded to the Alpha Quadrant.
- All borders, sovereignty and ownership of affected territory would return to its pre-war status as of Stardate 50564.0, when the first Dominion fleet entered the Alpha Quadrant.
The terms of the treaty largely left the Cardassian Union intact and unoccupied, with the exception of the territorial losses it suffered as a result of the Klingon-Cardassian War. (DS9: "What You Leave Behind")
Upon the signing of the treaty, Admiral William Ross remarked, "Four hundred years ago, a victorious general spoke the following words at the end of another costly war. Today the guns are silent. A great tragedy has ended. We have known the bitterness of defeat and the exultation of triumph. From both we have learned there can be no going back. We must go forward to preserve in peace what we've won in war." (DS9: "What You Leave Behind")
The prop for the treaty was put up for auction. The text of the treaty was repeated several times on the document.
The following conditions are inaugurated into this agreement by the United Federation of Planets, the Klingon Empire, the Bajoran Republic, the Romulan Star Empire, and the Cardassian Union of the Alpha Quadrant and the Founders of the Dominion of the Gamma Quadrant.
Effective stardate 52902.0, all hostilities by all armed forces under the command of each of the Alpha Quadrant and Gamma Quadrant powers are to be permanently ended.
A general ceasefire order will be ordered by each of the powers at that time. All military forces of the Dominion, including Founder, Jem'Hadar, Vorta, or other allies are to withdraw from the Alpha Quadrant effective 26 hours following the general ceasefire order. No Dominion military personnel, spacecraft, or materiel are to remain in the Alpha Quadrant without the express written consent of the joint Alpha Quadrant powers. All Alpha Quadrant territories presently under Dominion control, whether seized by force or by treaty, are to be returned to the control of the Alpha Quadrant powers. All borders, sovereignty, and ownership of affected territories are to revert to their status as of stardate 50564.0. This solemn declaration is simultaneously undertaken by the United Federation of Planets, the Klingon Empire, the Bajoran Republic, the Romulan Star Empire, and the Cardassian Union of the Alpha Quadrant and the Founders of the Dominion of the Gamma Quadrant.
The Treaty of Bajor is referenced in the novelization of What You Leave Behind as well as the Star Trek: Voyager novel Ghost Dance. According to the Star Trek: Deep Space Nine - Mission Gamma novel This Gray Spirit, the Allied Tribunal (β) negotiate a further series of treaties with the Dominion known as the Dominion War Accords, which among other issues, deal with the level of aid given to the Cardassian Union.