Having lost both her parents in a car accident when she was very young, Naoto is an orphan who acts very mature in spite of her age. As a descendant of a respected lineage of famous detectives, she wears formal clothing and deepens her voice when she speaks in a sophisticated, stilted manner. She is generally very serious, focused and mission-oriented. She rarely jokes around which can make her seem like a killjoy or party pooper when the team is involved in silly antics. In Persona 4 Arena, Kanji calls her out on this, saying she is too "uptight" and it makes her seem distant and on a different wavelength.[1] One of Naoto's insecurities is her lack of friends; she has difficulty making friends and is lonely as a result.

Naoto is very intelligent and analytical. A running gag, however, is that she texts in all caps with abbreviations, for example, "SEE U TOMORROW? Y/N PLZ REPLY ASAP" and "I HAVE IMPORTANT INFORMATION 4 U, PLZ SEE ME TOMORROW AFTER SCHOOL"

Naoto's insecure about her gender and age: she yearns to be seen as an adult, and expresses frustration at being treated like a child by the police force. She hates being looked down upon, and fears no one will take her seriously as a female in a sexist occupation field. The sexism Naoto has tolerated and endured had made her self-conscious and ashamed of being female, making her struggle with the concept of femininity. In response, Naoto desired to be male; Naoto wanted to be viewed as male by society, adopted a male identity, never corrected anyone when people used male pronouns, avoided feminine clothing and wears platform shoes to appear taller. It is also implied Naoto began binding her chest to hide her breasts.

After dealing with her Shadow, Naoto decides to give being female another try. However, Naoto still has difficulty accepting it in her Social Link. By the end of the game, due to her own will and with the protagonist's help, she accepts herself for who she is, and the fact she does not always need to change who she is to suit the world. In the epilogue of Persona 4 Golden, she has started dressing more freely, disguising her femininity less than before. She is comfortable with not only who she is, but also that everyone else is aware that she is female.

Despite her mature nature, Naoto has a shy side to her, as she refuses to wear a bikini at the Yasogami Beauty Pageant, but still manages to win despite dropping out of the swimsuit part because of her endearing popularity among voters. She also becomes embarrassed during the Investigation Team's visit to the Amagi Inn, when the schedules for the hot springs' use were confused. During the ski trip in Persona 4 Golden, Naoto appears to be afraid of ghost stories, and when in a state of fear and/or panic, her voice becomes more feminine than usual, possibly meaning she only has a masculine voice when she is composed. Unlike the other girls, she is shown to be a decent cook as she helped create an edible and delicious cake for Nanako's recovery celebration, though this was mostly down to her insistence that she and the other girls follow the recipe and admits that it took them three attempts to get the desired result.

Naoto is uninterested in romance, and seems easily flustered, embarrassed or dismissive when the topic arises. When she possibly receives a love letter, Naoto claims romance is "entangling" and she has no time to be "dilly-dallying with callow love affairs" and almost throws it away. However, she is willing to date the protagonist if he advances her Social Link.