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",[7] 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.[8] 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.[5] Inversely, he prefers not to involve allies who are not part of the Gotei 13 (particularly humans), as he requested Ichigo Kurosaki to move to safety, and did not request for Orihime Inoue to repair the left arm he sacrificed for Ittō Kasō.[9]

Despite his stern and steadfast personality, it is not to say he has no compassion and admiration, even for his enemies, as he was reluctant to strike down Wonderweiss Margela for his childish form and personality (only managing to get through this when Wonderweiss' Resurrección makes him no longer look like a child),[10] and felt pity for him that Sōsuke Aizen stripped him of all his higher mental capacities except emotions (mainly fear of death).[11] He commended the Tres Bestias for their bravery of attacking him with only one arm each, and struck them down without killing them.[12] Yamamoto felt particularly furious when Driscoll Berci utilized his lieutenant Chōjirō Sasakibe's stolen Bankai, considering the inferior power to that of the original wielder as an insult to Chōjiro's memories and hard work; Yamamoto brutally burned Driscoll to cinders, showing his immense respect for a longtime friend and subordinate.[13]

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.[14]

Yamamoto was apparently shameful of his past actions. He once referred to a painting of his past self as a monster that brought the Soul Society further turmoil when it was in a period of instability.[15] Yhwach noted 1000 years ago, Yamamoto was a demon himself, using any necessary means to defeat his enemies, and treated Humans and his own subordinates alike as expendable pawns; it was only after defeating the Quincy and attaining peace did Yamamoto live with honor and justice that led him to hesitate in sacrificing people heedlessly.[16]