Following her appearance, Makoto received a positive reception, often being highlighted as a fan favorite character, with critics praising the voice acting by Leigh and Satō respectively, her design, and her strong convictions.

"[5] Makoto first appears in Persona 5, tasked with uncovering the identity of the Phantom Thieves by her principal in exchange for a good recommendation for a university.

She starts following people she believes suspicious, including Joker, Ryuji, Ann, and Yusuke, eventually discovering their true identities as the Phantom Thieves.

Makoto joins them as a Phantom Thief after infiltrating his Palace, defeating his Shadow and forcing him to confess his crimes after taking his heart.

Her sister, Sae Niijima, works as a prosecutor investigating the Phantom Thieves, and butts head with Makoto over her feelings on the goodness of the group.

Makoto discovers that Sae's true feelings are to view trials as games to win by any means, and she eventually defeats her, convincing her to change her ways.

Makoto and the others also discover that Akechi had been setting them up, eventually managing to trick him and defeat him, as well as Masayoshi Shido, a man whose goals would destroy Japan.

She regards her as a stark contrast to fellow protagonist Ryuji Sakamoto, due to his brash and hot personality and felt that his fans would dislike her, and vice versa.

[12] Writer Nicole L. Rowe discussed Makoto and her Persona awakening moment as being intertextual with her, as well as how her interactions with Kaneshiro tie into issues of sex trafficking in Japan.