The First Church in Malden was gathered in 1648 from settlers in Mystic Side who wanted to separate from Charlestown and its First Church due to the distance needed to be traveled from their settlement to the church every Sunday. In 1649, the settlers were given official consent to incorporate and form both the town of Malden and the First Church in Malden. The first pastor of the church was Rev. Marmaduke Matthews whose call created tension between the church and the ruling General Court due to his ordination and theological beliefs before he left in 1652. Matthews was followed by Rev. Nathanael Upham then Rev. Michael Wigglesworth in 1655 who became known for his poetry including “The Day of Doom” in 1662 before his death in 1705. These first three ministers preached in the first meeting house before it was replaced by a new larger meeting house in 1658. The second meeting house was enlarged multiple times when the congregation grew too large for the building, including in 1702 and 1721. After Wigglesworth and when he was unavailable due to illness, various supply pastors served the church with Rev. Thomas Cheever being ordained as pastor for 1681-1686 before Rev. David Parsons became minister in 1709 until 1721. In 1721, Rev. Joseph Emerson, namesake of the Emerson School and ancestor of the famous poet, became minister and remained until his death in 1767. In 1729, due to expanding town borders and population, a third meeting house was built on a new site which was more centrally located, but this caused tension with those in South Malden (now Everett) who decided to separate in 1730 and begin services in their own building as the Second South Church in Malden in 1734. In 1792, the Second South Church rejoined with First Church with Rev. Eliakim Willis from the Second South Church becoming minister of the now united church until his death in 1801. Before Willis, Rev. Peter Thacher, known for his role in the Revolutionary War and early Massachusetts history, was ordained as minister in 1770 and remained until called to the Brattle Street Church of Boston in 1784 with Rev. Adoniram Judson following as minister of First Church in 1786 until the opposition to his theological views caused him to leave in 1791. To assist Willis, Rev. Aaron Green was called in 1795 and remained until 1827 when he left due to rising tensions between the Congregationalists and Universalists. In 1803, with the growing prosperity of the church, a fourth brick meeting house was built, but it was kept by the Universalists who formed the First Parish in Malden in 1828 after the Congregationalists spilt from the parish due to theological differences and the calling of Universalist minister Sylvanus Cobb.

After the First Church split, services were held in upper rooms with various supply ministers until Rev. Alexander Wilson McClure was ordained in 1832 as both pastor of First Church and minister of the Trinitarian Congregational Society of Malden, an ecclesiastical society organized in 1832. Also in 1832, the first women’s society began under Mrs. McClure with the Female Benevolent Society, a new church building was built by the Trinitarian Congregational Society, and in 1833, the Sunday School started. In 1850, the church building was moved closer to the center of town with services beginning in 1851 and lasting until 1869 when the building was destroyed by a September gale while in the process of being expanded. McClure remained pastor until 1842 when he resigned due to ill health and was followed by Rev. Chauncey Goodrich from 1843 to 1847 before McClure recovered and returned in 1848 until 1852. After McClure, Rev. Aaron Chester Adams was pastor from 1852 to 1857 followed by Rev. Charles Edward Reed from 1858 to 1869 then Rev. Addison Pinneo Foster from 1870 to 1872. In 1870, a new church building in the Gothic style located on Pleasant Street was completed with a dedication in 1871. In 1874, Rev. Joshua Wyman Wellman became pastor and oversaw a period of growth and prosperity in the church along with various changes in church procedures until his resigning in 1883 though he continued to interact with First Church and Malden and wrote “The Ecclesiastical History of Malden” in 1890. After Wellman, Rev. Theodore Claudius Pease, known for his sermons and hymns, was installed in 1884 and saw continued growth at First Church until his resignation in 1893 with the church’s prosperity and changes then continuing under Rev. Henry Hugh French from 1894 to 1914 and Rev. John Francis Dobbs from 1915 to 1925. In 1920, the Trinitarian Congregational Society was dissolved and incorporated with First Church into one entity allowing the church freedom to govern itself. In 1925, Rev. Roy Linden Minich, known for his involvement in both the congregational denomination and Malden along with his authorship, became minister and remained until 1956 when he was made the church’s first Pastor Emeritus until his death in 1975. In December 1933, the Gothic church building burnt down completely along with the majority of items within it.

During the various periods of growth and change in the 1800s, many members left First Church to form other congregational churches while others started missions or Sunday schools in areas around Malden. Outside of the Second South Church, the earliest related church was the First Congregational Church in Melrose, which began in 1848. It was followed by the Winthrop Church in South Malden also in 1848 which became the First Congregational Church in Everett after merging with the South Malden Congregational Church in 1870 before closing in 2013. In 1852, a mission was started in Edgeworth as a Sunday school with Edgeworth Chapel being built in 1866 before it was sold in 1922 to the Catholic Archdiocese with the missionary work moving to the parsonage and recombining with First Church. In 1873, the Maplewood Congregational Church split off as an independent church until 1978 when it closed and rejoined with First Church. Following Maplewood, the Linden Congregational Church began in 1876 and rejoined First Church in 1969. In Forestdale, a desire for a church school led to a mission in the area and the building of Forestdale Chapel in 1892 which continued to grow as a church and Sunday school until 1933 when it became an independent church as the Forestdale Community Church. The last church to split from First Church was the Mystic Side Congregational Church in Everett in 1893 which received members from First Church in Malden, First Church in Everett, and other churches.

After the 1933 fire, the eighth and last church building was completed in 1934 on the same site with various renovations since then to accommodate modern amenities and the changing needs of the church. In 1956, Rev. Walter Bruce Lounsbury was called before suddenly dying in 1959. In 1960, a chapel was built and dedicated based on plans made by Lounsbury as part of a newly constructed education building that took the place of the old Parish House. Also in 1960, Rev. William Patterson Gray became minister until 1974 during which time the church grew in membership, programs, and outreach. In 1975, Rev. Clifford Tobin became minister but was terminated in 1977 due to tensions between the congregation and ministerial staff. In 1978, Rev. Harold Landwehr became minister until 1987 with Rev. Randall Ferrara following in 1989 until 2009 and Rev. Patrick McCorkle in 2012 until closing. In August 2014, a fire damaged the front of the building, and the building was sold in August 2015 to the Jefferson Group though services continued for a short time. Throughout the 2000s, membership and finances declined, and while the church tried to continue and revitalize in various ways, it closed and was demolished in 2016.