Bean was born in Alton, New Hampshire. His parents were John and Elizabeth (Hill) Bean. He attended Friends Boarding School in Providence, Rhode Island. He moved to Iowa in 1853, where he taught school in West Branch.
Bean met Hannah Elliot Shipley from Philadelphia, Pennsylvania, during a trip she took to Iowa. In 1859 they got married at the Orange Street Meeting House in Philadelphia, Pennsylvania, and settled back in West Branch. They visited the Sandwich Islands (Hawaii) from 1861-1862 as Quaker ministers. Joel was appointed clerk of the Iowa Yearly Meeting (Iowa YM, see Yearly meeting) in 1867, and the couple went on a ministry tour of Europe from 1872-1873.
When they returned from the trip to Europe the Beans discovered that the revival that had been springing up among Friends in Iowa had progressed to a point that they could not approve. The revivalists insisted that people need to be “saved” and “sanctified,” which the Beans and others did not think was in accord with traditional Friends beliefs. The revivalists were also bringing into their meetings such things as programmed (planned) worship, more emotional worship, and paid pastors.
The Beans at first had welcomed the revival movement, believing that it was bringing life into the Society of Friends. But they saw that as it progressed it was departing from such Quaker ideas as the universality of the Inner light, the need for spiritual discipline and gradual growth rather than instant perfection, silent meetings for worship to wait on direct and personal guidance from God, and volunteer lay ministers and elders.
Even though the Beans opposed the holiness movement, they would not join a group of Conservative Friends who left the Iowa YM in opposition to that movement. They disliked division and did not want to be part of it. After moving to San Jose, California for the sake of Joel’s health and meeting with other Friends there who had been a part of the Iowa YM, they helped to establish the College Park Association of Friends. Then in 1893 the Iowa YM deposed them as ministers and in 1898 disowned (expelled) them from membership altogether.
Many Quakers in England and New England were shocked and unhappy about the Beans’ disownment, as the Beans had proven themselves devout Friends and apt ministers. The New England YM accepted them as members and as ministers.
Joel and Hannah Bean’s granddaughter Anna Cox Brinton was influential in the development of the Pacific YM from the earlier College Park Association.