In September 1956, Bishop Charles Buddy of San Diego appointed Fr. Flynn as the pastor of St. John the Evangelist, Riverside. Gathering a small community, Fr. Flynn celebrated the first Mass on September 16, 1956, in the chapel of Rubidoux Mortuary. The new parish community consisted of 46 families.

A plot of ground was purchased at 3980 Opal Street on All Saints Day, and the old house on the property was converted into the rectory, chapel and office. While the church was under construction, the living room provided the setting for the celebration of daily Mass, marriages and baptisms. This building is still in use as the Parish Office. In December of 1957 Bishop Buddy made the trip rom San Diego to preside at the Mass, which celebrated the dedication of the new church.

The vision of a parish school became a reality in 1961, as ground was broken for its erection. In June of 1962, the Dominican Sisters arrived to staff St. John the Evangelist Elementary school. After a decade of providing Catholic education to many children, the school unfortunately closed. Since that time, the classrooms have provided meeting space for Religious Education classes as well as various other parish ministries and organizations. St. John the Evangelist Parish serves Our Lady of Guadalupe Mission, Belltown, which originated in 1927.