The Captain's Quarters is located in the aft section of every ship. The Captain's Quarters of each ship is quite different, with their current only common feature being the Voyage table and Shelves. After buying Voyages from one of the three Companies, voyages can be placed and voted upon on the Table in the Captain's Quarters. Once started, both voyages and Tall Tales can be canceled here. The shelf is technically just a decoration, but it is often used to "store" small treasure (skulls, trinkets, mermaid gems, etc.).
The Captain's Quarters of the Sloop is right below the helm, covered by a sailcloth (the color of which depends on your ship Livery, not the Sail type). This area offers a passage between the lower and top deck, but is quite cramped due to limited space. The Captain's Quarters of the Sloop houses the Voyage table, a Shelf and Barrels on the left-hand side for smaller treasure placement, a Weapon and Ammo Chest right by the stairs, a window on each side for taking shots out of or bailing water (make sure you aim the water out of the window, not above, otherwise the water will hit the window covering and splash right back in the ship), a Map Table right under the sailcloth (allowing the solo captain to quickly check the map from right behind the Helm above) and a Rowboat dock right behind the Map Table. This area on the Sloop can sustain damage from cannon fire. The holes in the Captain's Quarters do not fill up the ship with water very quickly as it is above the water level, however the more damage the ship receives, the more dangerous these small holes become.
The Captain's Quarters of the Brigantine is situated right behind the stairs of the bottom deck and is even more cramped than the Sloop's, having more decorative elements such as a bed, a white drape, a non-interactable chest and a windowed wall separating the quarters from the rest of the ship on one side. The only common element here is the Voyage table and the smaller Shelf for placing trinkets. Due to its cramped nature, the Brigantine's Captain's Quarters is an excellent place to hide your treasure or maybe even yourself when on an enemy ship. The most common hiding spot is right behind the windowed wall and the Voyage Table. Despite the bottom of the stairs being open and spacious, no items can be placed under it. As with the sloop, the Captain's Quarters of the Brigantine can sustain damage from cannon fire. Similarly, the holes in the back will not fill up the ship with water as fast as holes in the front, however they should be tended to at once, as the Brigantine only has one bottom deck and will fill up very quick if left without attention. Due to the drapes and the bed taking up all of the space at the back of the ship, the holes that appear behind them can be tricky to plank from an angle.
The Captain's Quarters of the Galleon is the most fleshed out of the three. It is a fully decorated separate room situated right below the Helm. It is accessible from two doors, one on the front (leading to the main deck) and one on the left side (leading to the balcony and Rowboat Dock). The only actually interactable item in the Galleon's Captain's Quarters is the Voyage table, with the rest filling merely decorative purposes. Interestingly enough, despite there being a single Lantern that can be extinguished and lit in the Captain's Quarter, there is also a chandelier and a handful of candles that cannot be extinguished, making it impossible to darken out the room on a Galleon. The main decorative elements of the room are a bed, a shelf, two cupboard, two chests, a bookcase, a throne, four windows, a galleon miniature, two birdcages and a shark jaw bone trophy. The Captain's Quarters on the Galleon is mainly used to stash and hide treasure (or yourself, if on an enemy ship). The main treasure stashing spots are behind either side of the door, either on the bed behind the door, on the chest on the other side or behind the throne. More experienced pirates have been seen to expertly hide treasure on top of the door or the chandelier. The Captain's Quarters of the Galleon also allows access to the rear balcony. The balcony doubles as a rowboat dock.
At the end of a Lost Shipment voyage, when a crew finds the sunken Merchant Alliance galleon, there will be a locked Captain's Quarters where a normal Galleon's quarters is located. This can only be opened by finding a Captain's Key in one of the modified Barrels of Plenty, and is optional. Upon entering, the crew will find a large pile of Trade Good Crates and a Gunpowder Barrel to sell along with the Merchant Manifest. However, if a crew wants to use the Captain's Key, it is advised to not pick up the Manifest until after the Captain's Key has been found, as grabbing it will end the voyage, despawning the key, wherever it is.