In scholarly works, his name is generally romanised as "Eizi Matuda" following the "Kunrei" system.

Matuda and his wife, Miduho Kaneko de Matuda, were naturalized Mexican citizens and had five Mexico-born children.

[1] In 1956, a species of cactus native to Mexico was named in his honor, the Mammillaria matudae.

The genus Matudina in the sunflower family is also named in his honor.

[2] Two species and one subspecies of reptiles are named in his honor: Abronia matudai (Matuda's arboreal alligator lizard), Anolis matudai (Matuda's anole), and Pseudelaphe flavirufa matudai (Matuda's ratsnake).