Other than the bridge itself, the interior of the player's ship may be visited to a very limited extent, and customized to a very limited extent. The player may invite other players onto the bridge of his vessel, and from the bridge the owner of the vessel and any other players he chooses to invite aboard may proceed to access the other interior spaces of the ship via the turbolift.
Barring the extremely limited customization options available to the player, all ship interiors are identical save for a few randomly-selected plants and fixtures. Every vessel in Starfleet, from a tiny Defiant to the huge Galaxy-X dreadnought and the majestic Star Cruisers, will have the same interior furnishings, which can be immersion-breaking considering that the engine room of a Sovereign-class starship wouldn't really fit in a Defiant-class Escort.
The customization options which are open to the player for modifying the ship's interior are simple: in major space docks (Earth Space Dock and Deep Space Nine for example,) from the same NPC and menu selection that one chooses to modify one's bridge, one may also choose to modify the ship's layout, choosing from your selection of Small, Medium and Large, of which the default is medium, and a change in layout costs 1,000 Energy Credits. The layouts only affect the amount and lay-out of the corridors in the Crew Decks and Engineering, they do not "shrink" the rooms or alter the rooms which get tacked-on in any way; in effect, the only difference is how much distance one has to travel to get from room to room.
 Command Deck
The Command Deck is typically Deck 1 on a starship. It is from the main location on the Command Deck, the Bridge, that the captains direct their vessels and command their crew. There is, however, one other location of note on the command deck.
 Ready Room
The Captain's Ready Room is where the captain of a starship waits until he is needed when he is on-shift but not needed on the bridge. It contains a desk for the captain to get work done on, a couch upon which the captain may rest, a few trophies of past deeds or mementos to starships gone by - or the starship being flown - and is, generally speaking, the captain's business office. In the Star Trek canon, these Ready Rooms vary greatly by the captain's taste; some preferred to keep a pet such as a housecat, which would usually have a warm lounge for it, while others preferred a fish-tank or terrarium, while some might prefer works of art or mementos of home.
In Star Trek Online, there are three models of Ready Room available: the default, the TOS conference room, and the Belfast model. The furnishings are largely fixed; while the pictures on the walls (which are in fact screenshots of Star Trek Online, and no they are not chosen from the player's own screenshots) and the exact type of plants may vary, the player will always have a picture on the wall and a plant in the same location. The player's desk and lounge area will always be the same, barring the player's own choice of wall trophies, which may be ship models or related to accolades the player has earned, and the player's fish-tank will always be the same.
The computer on the Captain's desk is the only part of the ship interior that serves a non-social function, allowing the player to access diplomatic and military assignments.
 Crew Deck
The Crew Deck is an abstraction for any number of decks upon which the crew of a starship might reside, depending on the exact size of the deck; it may be adequately surmised to be only one discrete section of the crew decks that coincidentally happens to contain the three realized locations of the crew deck interior: the Lounge, Captain's Cabin, and Sickbay.
A gathering place for the crew in off-hours, the Lounge may at times be used for some official functions, such as weddings performed by the captain. Ten Forward, found on Deck 10, Section 1 of a Galaxy-class starship, is a prime example of a ship's lounge.
The Lounge has a much larger trophy wall available to it than the Captain's Ready Room, with space for four wall trophies and a floor trophy, which is typically a monumental trophy relating to the successful completion of a story arc, though alternate trophies consisting of Gold-Pressed Latinum may be purchased with GPL from Woadroh "Woadie" Bhoith, a vendor in Quark's Bar on Deep Space Nine, or Greelan, a vendor in the gambling hall on Drozana Station
In addition, there are some NPCs giving access to development assignments:
The counselor resides in the lounge, giving the possibility to start psychological sessions for medical and development CXP.
Cooking chain assignments are available by the chef, plus bartending chain assignments by the bartender.
 Sick bay
- Not to be confused with Assignment: Sick Bay.
The sick bay of a starship is where medical personnel care for sick or injured members of the crew. Given the rate at which crew members become injured during battle, one might surmise that this is one of the most heavily-trafficked locations on the ship. However, you probably won't be spending much time here, because there's not that much you can do in sick bay.
 Things you can't do in sick bay
Don't expect your sick bay to work like it does on the television series. The Emergency Medical Hologram cannot be activated by the player when visiting sick bay. Also, if you have any duty officers who are currently performing the “Sick Bay” assignment, they cannot be seen when you visit your ship's sick bay. Therefore, you can't "visit" injured colleagues, like a good captain should. Truth be told, the whole area is fairly non-interactive, at least as of Season 6.
 What's it good for, then?
Whether you'll find sick bay a useful place depends greatly on the kind of player you are. Most players will probably find it practically useless. However, if you have the right duty officers, and you're sitting on a lake of dilithium, it can be a way of buying your way to Development commendation point success.
The doctor in sick bay basically just gives you the same assignments available from the Medical tab of your duty officer menus. However, he also gives you two, 5-minute assignments — “Assemble Hypo Pack” and “Assemble Medical Regenerator”. These are worth 50 Development CXP, and cost either 5 or 25 dilithium. For the time and dilithium invested, they have a pretty huge return of CXP. Given that these assignments are literally right across the hall from the Bartender's “Pour a Drink” and “Special Reserve” assignments, you can easily pick up 200 CXP in five minutes by running back and forth between sick bay and the lounge. If you critically succeed, that number can grow to 1000 CXP — again, for five minutes' work. So sick bay is not entirely useless.
Also, you might actually want the items produced by successful completion of “Assemble Medical Regenerator”. If you or one of your bridge officers sustains an injury, then you don't have many options. Either you go to a starbase 's Chief Medical Officer, or you get a regenerator of some kind. If you haven't been dropped a regenerator, or bought one on the exchange, then you can either go back to a star base or you can go to your sick bay and run “Assemble Medical Regenerator”. Of course, it costs 25 dilithium to run the assignment, so it's not the cheapest way of getting a regenerator — but the CXP reward sweetens the deal.
 Captain's Cabin
The Captain's Cabin are the quarters which the Captain of the ship may call his or her own; two rooms have been realized, a large, open cabin containing a broad seating area of couches and chairs along the windowed wall, a large dining table and a desk for the captain, and a smaller bedroom containing a bed, replicator, and various fixtures such as chests-of-drawers and potted plants. As usual the plants and paintings in the captain's cabin will by randomly chosen on a new ship, but the player is unable to customize the Captain's Cabin, not even with wall or floor trophies in the vein of those found in the Lounge or Ready Room.
The Engineering sections of a starship are vital for a starship's operation; they contain the Main Engineering bay, home of the ship's power generation, a Science Lab and a Transporter Room.
 Main Engineering
The throbbing heart of any starship, it is within Main Engineering that the Matter/Antimatter Reaction Assembly that compromises a starship's Warp Core is installed, providing primary power generation for all of a starship's functions, including (obviously) warp drive.
In Star Trek Online, the only realized Main Engineering bay on Starfleet vessels is that which appears on the Sovereign-class starship U.S.S. Enterprise (NCC-1701-E) beginning with the movie Star Trek: First Contact, regardless of how comically incorrect it would be to find this engineering bay on a ship over a century and a half old or not large enough to contain the bay or worse, both.
The Chief Engineering officer gives access to engineering assignments, even such that reward components, Mk XII consoles or turret prototypes.
Colonial and some trade assignments are availably by the Operations officer. This also goes for assignments of the Colonial chain.
 Engineering Lab
The Engineering Lab — formerly known as the Science Lab — will be of great interest to players who want to improve their Science commendation point standings — or their tribbles. It's also a great place for players who like to collect data samples but don't particularly enjoy crafting. However, it is likely a place that combat-oriented players avoid or simply misunderstand. If you are even slightly interested in improving your science standing, the Engineering Lab is a better place to spend your time than combing through the assignment list.
Furthermore, the assignments on offer here are unique. It's the only place where you can accept assignments to:
- make better tribbles
- adapt Strange Alien Artifacts
- use large quantities of practically all data sample types outside the crafting module
Approach the scientist on duty to get a full list of all available assignments. When his dialogue box pops up, enquire about his "special projects". This will then give you the opportunity to explore all three of these unique opportunities.
All of the data sample analysis assignments award around 1000 points — either wholly in science, or split between science and exploration. Assignments last only between 6 and 8 hours, though they do require significant numbers of data samples.
Tribble and Strange Alien Artifact assignments are less profitable, but they also take much less time, and require fewer inputs. Those that enjoy the tribble module will doubtless enjoy the wide range genetic variations available for their fur balls. The Infuse Alien Artifact with Rare Particles option allows you the opportunity to do something with the Strange Alien Artifact that you picked up after completing the "Children's Toys" assignment chain.
 Transporter Room
A ship's Transporter Room needs little introduction; it is from these transporter pads that crewmembers, including the Captain, are converted to energy and rematerialized in another location, be it a starbase or the surface of a planet or another ship. Occasionally, crewmembers will walk onto the transporter pad and beam themselves elsewhere, and sometimes crewmembers will likewise materialize on the pad from parts unknown. The player who owns the ship will also find an NPC in this area that will let them switch to a shuttle.
The ship's Turbolift system is the vital circulatory system that takes the lifeblood of a starship - its crew - to where they need to be. One merely steps into the lift and states one's destination (or enters it manually into the control panel,) and away one goes.
In Star Trek Online, the turbolift takes players between the three accessible decks of the starship - the Bridge, Crew Decks, and Engineering.
- It is a known bug that oftentimes a player to whom the bridge does not belong, when attempting to use the turbolift, will get ejected into space. A method of reducing the risk of this aggravating bug is to jump and press the UI button to go to one's desired deck, timing the press so that it takes effect as the character reaches the apex of their leap.
- If a player gets ejected into space, they can use the /stuck command to be returned instantly to the bridge of the ship from which they were launched, instead of waiting for Star Trek Online to return them on its own.