In 1801, a dispute arose between the officials of St. George's Methodist Episcopal Church and 80 male members of the church. These men petitioned Bishop Francis Asbury to remove Presiding Elder Joseph Everett from the city. When Bishop Asbury refused, 50 of the original group left St. George's and formed Methodist Episcopal Union Church. They rented part of Whitfield Academy for worship, which was located on 4th Street between Market and Arch. (Whitefield Academy also housed the University of Pennsylvania at this time.)

In 1802, Union purchased the south end of Whitfield Academy and in 1833, built a church on this site. In 1885, the church temporarily ceased services because of low membership, and later decided to consider mergers with other area churches. Still, a few members continued to worship at a private house located at 2026 N. 22nd Street in North Philadelphia.

One proposal of serious deliberation was from West Park Avenue Chapel, organized on March 22, 1878 and located on the northwest corner of Diamond and Woodstock Streets in North Philadelphia. The church was built by an independent religious society, under the leadership of a former Methodist and Lutheran pastor. Unfortunately, he was unable to pay for the church when construction was complete, and as a result, was confined in the city's debtor’s prison, as was the norm of the time.

On November 17, 1884, officials from West Park and Union convened a meeting and it was decided that the two congregations would merge. (The officials representing Union were George W. Wanamaker, A. J. Cliffe, John Canin, Christopher Bailey, W.J.P. Ingraham and G.W. Cook. It was also agreed that the two churches would unite under the name Methodist Episcopal Union Church, and that Union's pastor, Rev. Noble Frame, would preach separate services for the two congregations at their respective locations until the final merger. On the last Sunday in June 1887, the two congregations held its first public service together as one body in the West Park edifice.
 

On December 19, 1887, the Union edifice on 4th street was sold for $40,000 cash and the proceeds went toward the construction of a new edifice at the West Park location on Diamond Street. The cornerstone of the new edifice was laid June 4, 1888 at 3:00 p.m. Bishop William Taylor of Africa dedicated the building Sunday, February 17, 1889. The annex and the parsonage were added in 1894-95. The edifice was constructed by the prominent Philadelphia architectural firm of Hazelhurst and Huckel. The Romanesque design of the edifice utilizes monumental masonry with clustered columns and massive semi-circular arches. So impressed with this immaculate design, Mother Bethel A.M.E. church patterned the construction of its current edifice after this edifice. Methodist Episcopal Union Church closed its door in 1946 due to low membership and also the changes in the racial makeup of the North Philadelphia Community.

Today, the edifice has been traced to Benjamin Franklin and the founding of the University of Pennsylvania through The Whitfield Academy, once housed at this location. As a result, The United States Department of the Interior and The Commonwealth of Pennsylvania entered the edifice of Jones Tabernacle A.M.E. Church in the National Register of Historic Places on October 15, 1980.