- Deck 1 houses the main bridge. This deck also holds the more recent modifications of an observation lounge, a ready room for the ship's captain, and an airlock with attached cabin.
- Deck 2 encompasses the first of the many levels of crew quarters, with rooms for the highest-ranking command staff and an officer's mess hall.
- Decks 3 through 9 feature more officers' quarters, the forward and aft viewing lounges, science labs, the main shuttlebay, conduits for the optical data network, and the vessel's main computer core.
- Decks 10 through 14 complete the primary hull of the Sovereign-class starship, and also encompass forward and aft cargo bays on Decks 10 and 11, and phaser systems on Deck 11. Sensors and the secondary navigational deflector are found on Deck 12.
- Deck 14 is largely dedicated to engineering systems and feature the lower sensor platform. Decks 15 through 18 comprise the main navigational deflector array and an auxiliary bridge, which is also known as the battle bridge.
- Deck 13, is almost entirely taken up by deuterium fuel tanks and delineate the split between the habitable areas and the engineering / ship's storage sections. Main engineering and its related systems, such as the EPS power tabs, the central matter/antimatter reaction chamber, support labs, and the engineering computer core, are spread across Decks 14 through 18.
- Deck 16 also features the launch and retrieval mechanism for the captain's yacht. The yacht is lowered by a set of gantries until its engines extend to operational position and is then free to maneuver.
- Decks 24 and 25 contain the launch and loader mechanisms for the secondary hull's complement of quantum torpedoes and unmanned probes (fore and aft).
- Deck 27 houses the fore and aft tractor beam emitters.
- Decks 28 and 29 house the Antimatter reactant generator and storage pods, along with the lateral Phaser array.