Soto's first collection of poems, The Elements of San Joaquin, won the United States Award of the International Poetry Forum in 1976 prior to its publication in the Pitt Poetry Series in 1977. The New York Times Book Review also honored the book by reprinting six of the poems. In 1985, his memoir Living Up the Street received the Before Columbus Foundation's American Book Award.
In 1993, Soto received the Andrew Carnegie Medal for Film Excellence from the Association for Library Service to Children for his production work on the film The Pool Party. In 1999, Soto received the Hispanic Heritage Award for Literature, the Author-Illustrator Civil Rights Award from the National Education Association, and the PEN Center West Book Award for Petty Crimes.
Other honors include the "Discovery"/The Nation Prize, the Bess Hokin Prize and the Levinson Award from Poetry. He has received The California Library Association's John and Patricia Beatty Award (twice), a Recognition of Merit from the Claremont Graduate School for Baseball in April, the Silver Medal from the Commonwealth Club of California, and the Tomás Rivera Prize.
The library at Winchell Elementary School in Fresno was named after Soto.
In 2011, the Old Administration Building at Fresno City College became the permanent home of the Gary Soto Literary Museum.
In 2014, Soto received the Phoenix Award for his 1994 children's book Jesse. The award committee stated: "Jesse is both a coming-of-age story of one Mexican-American boy with a poetic sensibility and the story of a community and a country at a difficult time—facing poverty and prejudice and war, problems we are still facing today. Jesse offers an unembellished slice of life in Vietnam-era Fresno, California."