Patchwork Lab has very unique and eccentric architecture. The laboratory seems to almost always be under the veil of a purple sky with the moon grinning above it.
Patchwork Lab is a very large, blocky and slate grey-coloured building with multiple structures that make laboratory appear like a mix between a house's and a hospital building's architecture which all of the lab is surrounded by a grey wall. This wall has gap for the entrance, but on the ends of it, has two upward pointing arrows.
Like Stein himself, the building is also covered in stitches giving credit to its name, stitch markings that even cover walls of and even the grounds around the location, but also appear on the various experiments roaming the place. It has randomly placed windows with chain link fences and the structure itself looks very dingy and dirty as stains can be seen up close on the exterior walls. A wind-up mechanical mouse with patchwork markings crawls around the building.
One of the prominent parts of the building is a tower-like part in the shape of an arrow which can be compared to Medusa's Vector Arrows as well as a couple of dead, bare, stitched up trees located within the laboratory grounds, which have arrow-tipped branches. Around the entrance are a set of reddish double doors with a small set of stairs leading up to the doors accented with a purple fluorescent light on the right side of the doors. Two double-sided arrow motifs above the entrance pointing left and right of the laboratory can be seen as well.
The interior reflects Stein's emotionless desire for science and dissection clearly lacking in anything the slightest bit homely. Almost the entire colour scheme is grey with stitch marks present on the walls. In the anime, white arrows can be seen painted on the walls and floors, whilst in the manga, it is a tiled floor instead.
The building includes an operating room, filled with scientific and surgical equipment. Here, Stein has engaged in his more disreputable acts of vivisection, but here he also has aided in the medical recovery of students possessed by Shaula Gorgon, such as Eternal Feather and Meme Tatane. This operating room is also where he stored the corpse of Sid Barrett and where he likely turned the deceased meister into a zombie. After performing some medical procedures in the operating room, evidence of the procedures remain: blood covers the gauze, waste, and operating table.
Stein's building also includes a computer lab, shelves filled with files and books, and in the anime Soul Eater Not! a reception window.
Despite it being his living quarters along with being a laboratory, Stein does not have any basic living utensils, and only uses his science equipment for both scientific and daily needs. Referring back to the anime, a rather bland bathroom and bedroom is also shown. Although there is working electricity, Stein seems to prefer to do most of his work in the dark, foreshadowing Stein's tragic nature.
After Marie Mjolnir moves in, she as well as the audience notices the lack of living essentials and therefores adds more homely items to the laboratory, such as cups, sofas and a coffee table. Marie mentions that Stein gets annoyed if she adds too many things to his laboratory, so she gradually adds few by few to keep him calm.
- The interior of the laboratory, such as the furniture placing and the doors, change each time it is shown in the anime. Even the direction and placing of the arrows on the floor changes.