The founding of Jerusalem Mar Thoma Church, Kottayam is closely connected to the genesis of the Malankara Mar Thoma church itself. Inspired by the liberal ideas of the English missionaries, Palakkunnath Abraham Malpan, popularly known as the Luther of Malankara Church and Kaithayil Geevarughese Malpan made great efforts to make reformation in the Malankara Church, starting from the year 1836. This led to tumultuous decades and at the end of many dramatic events, the Malankara Syrian Church split into Jacobite Church and Marthoma Church, who were also called reformists. In the court cases for the churches and properties that followed, the Marthomites were denied all material possessions. The reformists wanted to build a church for their own in Kottayam instead of Old Seminary and Cheriya palli, which they lost in the court cases, and they started searching for suitable land in Kottayam. However, their opponents made all efforts to make sure that land was not made available for the reformist people. Since the land where the church now exists, which they found ideal to build a church was owned by Joseph Lawrence Gomez, who refused to sell the land to Marthoma people, two Anglican Church members helped to procure the land from him.