Yamamoto is the oldest captain in the Gotei 13. He has the appearance of an old man with red eyes, a very long white beard, and long eyebrows. There are many scars on his torso and head, the two most prominent being a pair of long, perpendicular scars above his right eye, left by his battle with his lieutenant. After his brief confrontation with Sōsuke Aizen, Yamamoto lost his left arm. He wears the standard Shinigami uniform, but its size is greatly exaggerated. He drapes his haori over his back instead of actually wearing it. Despite his old and frail appearance, he has a very muscular body which he only reveals when he goes to battle, something which Shunsui Kyōraku claims is not seen too often.
When he was much younger, Yamamoto had black hair on the sides of his head, and was bald on top. He had a tuft of hair sticking up at the back of his head in a topknot. He had thick black eyebrows and a long, thick black mustache. He had a single large scar on his forehead, which earned him the nickname "Eijisai" due to its shape. He had prominent wrinkles on his forehead and beneath his eyes, and shallow cheeks. He wore the typical black outfit of a Shinigami.
As the Captain-Commander of the Gotei 13, Yamamoto is highly respected by most of the Shinigami, most notably Sajin Komamura, who views Yamamoto as a benefactor who saved his life. The embodiment of conviction, Yamamoto follows the laws and regulations of Soul Society to the letter, and expects the same of others. He is not a man to tolerate insubordination, and is vocal with those who attempt to act in such a manner. He is quick to anger in the face of possible betrayal and can be quite aggressive in combat. He has a habit of referring to those he faces in battle as "youngster", and he refers to a battle as a "beating" or "punishment". When in a state of peace, he carries himself with an air of frailty, to the point where he fell asleep standing while awaiting Shunsui Kyōraku's arrival for a meeting. Due to years of experience, Yamamoto very rarely shows any sign of distress or surprise, usually responding by opening one or both of his eyes, which are partially closed slits for the majority of the time.
Yamamoto is very loyal to Soul Society, and takes his duties very seriously, expecting the same from the rest of the Gotei 13. His loyalty is so great, he is willing to sacrifice himself and the Gotei 13 in order to defeat Aizen, believing it to be their duty to lay down their lives for the sake of the Soul Society if necessary. Yamamoto becomes visibly angry when Shunsui, Byakuya Kuchiki, and Kenpachi Zaraki lose their haori and show little regret: to him, the haori represents their status as captains.
Yamamoto appreciates Eastern cultures, and is a master at the Japanese tea ceremony. He dislikes the Western traditions preferred by his lieutenant Chōjirō Sasakibe. Yamamoto holds a tea session every month in the 1st Division quarters for every member of his division. He plaits his own beard and arranges its ends once a month, and likes to be rubbed down with a dry towel while exposed to the sun on his balcony.