St. John Coptic Orthodox Church was founded in 1988 by a group of Copts who moved eastward from Los Angeles into the San Gabriel Valley area. Services were held in a rented church and a school in West Covina until the present parcel of land was purchased in 1990.

In 2004, the congregation built a large church in the modern Coptic style and His Holiness Pope Shenouda III – the 117th Pope of Alexandria – consecrated the church the same year.

Several priests served the church, including Hegumen Father Tadros Malaty, Hegumen, Father Bishoy Ghobreial, Hegumen, Father Felimon Mikhail, Father Markos Hanna, and the late Father Youhanna Alexander. Hegumen Father Gawargious Kolta and Father Augustinos Hanna both joined the church in 1989; Father Shenouda Ghattas joined in 2005 while Father Daniel Habib was ordained for the church in 2008. Father Youhanna Maurice Youssef joined the church in 2018.