In 1893, with the opening of the World's Fair, Dowie opened Tabernacle Number One which came to be called "The Little Wooden Hut" across from the entrance to the Fair. Dowie’s Divine Healing Association was not recognized as being a church so he was denied a place on the Avenue of Churches at the World's Fair. The first year at his mission was very hard and it was not until the niece of Buffalo Bill Cody, Sadie Cody, received her healing that the crowds began to come. He preached in the afternoons not wanting to interfere with the regular Sunday services of the mainline churches. Interest in Dowie's sermons was such that he was able to lease one of the largest auditoriums in Chicago for six months, from October, 1895 to April, 1896. During this time, Dowie proposed the organization of a church based on apostolic principles, and in February, 1896, he organized the Christian Catholic Church in Zion.

After the organization of the Christian Catholic Church in Zion, he dreamed of a city where his congregation would be free from the evils of the world, a city where God would be the ruler. He first looked for land south of Chicago in the Blue Island area, but the land was not suitable so he looked north of the city. In the fall of 1899, Dowie visited the land north of Waukegan and envisioned what he would come to name "Zion City". After successfully securing options on approximately 6,600 acres of land, he unveiled his plan for Zion City at the Watchnight Service the eve of the New Year 1900. It would be a city where his congregation could worship, work, and play free from the temptations of the world. Zion City was the only city, besides Washington D.C., that had plans completed before the first spade of dirt was turned. There would be places of employment - he imported a lace mill from England — schools, and recreational facilities, all controlled by John A. Dowie. The land would be leased to the people, with definite restrictions, for 1,100 years. Dowie reasoned that Christ's return was to be within 100 years and then the millennium, after which there would be no need for leases.
The people would share in the profits of the industries in Zion City and the profits, tithes, and offerings would be sufficient for the support of the Christian Catholic Church in Zion.

On July 14, 1900, hundreds of people came to what would be Zion City
for an all day affair which culminated in the dedication of the City to God.
The next year was spent surveying the city, laying out all the lots, planning for the utilities, and preparing for the opening of the City to the people. July 15, 1901 was the date that the City lots were made available to the public. The first house was built shortly thereafter in August, 1901. Dowie and his family came to Zion City from Chicago in July, 1902 and moved into Shiloh House, his newly constructed home.

Zion City never reached the potential that Dowie dreamed of having suffered financial troubles early on. In September, 1905, Dowie suffered a stroke and never fully regained his strength. While in Jamaica trying to regain his health, Dowie recalled Wilbur Glenn Voliva from Australia to be the Deputy General Overseer giving Voliva full power of attorney. With Voliva’s arrival in Zion City, he became aware of the dire financial condition of the City. He took steps to relieve Dowie by exercising the power of attorney given to him by Dowie. Dowie was asked to quietly resign from his office of General Overseer. Dowie chose not to relinquish control and a court battle ensued. The court ruled that the people could choose the successor and the great majority chose Voliva. Dowie was deposed and spent the last year of his life at Shiloh House surrounded by a small group of loyal followers. He died at Shiloh House in March, 1907, a few months before his 60th birthday. He is buried in Lake Mound Cemetery, Zion, Illinois.