The Port Mafia Base (ポートマフィア拠点, Pōto Mafia Kyoten?) consists of five tall, black buildings in the center of Yokohama. The main building stands at the forefront of the other four, looking over the entire city.
The headquarters have been active since over eight years ago, formerly under the previous boss' leadership. Since Ōgai Mori murdered him, all buildings are under his ownership.
The five buildings stand in the center of Yokohama, noticeable from a considerable distance due to their height and location. Notable landmarks nearby include Cosmo Land and the InterContinental Building. All five buildings are tall and black, similar in height, but the main one being the most prominent and tallest of them all. It contains a glass elevator that one can see the entire city from.
Mori's office likely stands on the topmost floor. Large doors lead up to it. Inside, it is a vast room with much empty space, whilst in the back Mori lines the walls with shelves of books and his desk and chair. Because of the clothes seen sprawled around, it is likely Mori has a stash of Elise's wardrobe in the room as well.
Generally, the room is well-lit by natural light thanks to large windows, however, there are automated shutters that encase the room in near-complete darkness.
Osamu Dazai's office from his time in the mafia is most likely located in the main building as well. From what is seen of it, it consists of a relatively simple and plain room with empty space, save for his desk and chair. The room is decorated with an obscure painting, and along with windows, has a candle on the wall to provide light.
The torture and the captive area lie in the very belly of the main building. Everything from walled handcuffs to torture and interrogation tools fills the room. The room has brick walls and - likely from all the gruesome acts held there - fairly grimy. It doesn't appear to be particularly large and has dark lighting.
Hall of Light and Dark
The Hall of Light and Dark is a dark hallway, illuminated by the light coming through tall stained-glass windows. It is seen multiple times throughout the anime: when Dazai finds out Chuuya is under Kouyou's command, when Kyouka asks Akutagawa to cut Demon Snow and kill her, and when Kouyou reveals she spent half a year's worth of Port Mafia funds to give Kyouka a gift.
Port Mafia uses an accounting facility as a place for money laundering. 
- Bungo Stray Dogs Anime: Episode 14.