[1] He served for a year as the first president of another Methodist school, Marvin College in Waxahachie, Texas, then completely retired from church-related work.

This conference assigned John and his wife Matilda [b] as missionaries to the people of the Choctaw Nation, who had just been removed from their homes in various Southeastern states to the Indian Territory.,[4] p. 13.

[c] In 1836, Matilda became a teacher in the first school for girls opened in the Choctaw Nation of Indian Territory (near Shawneetown in present-day McCurtain County, Oklahoma.

[3]) Suffering from poor health, Reverend John W. P. McKenzie retired from missionary work in 1841 and moved to a 421-acre (1.70 km2) plantation 3 miles (4.8 km) southwest of Clarksville, Texas.

For example, B. F. Fuller, a Baptist, admitted later that he was nervous about enrolling in McKenzie College and the difficulty he anticipated having there because of doctrinal differences.

In June 1861, McKenzie cancelled the final examinations and the graduation ceremonies that normally ended the school year.

Unable to keep the institution financially independent, McKenzie and his son-in-law, Smith Ragsdale, closed it on June 25, 1868.

[1] Giving up on restoring his school, McKenzie accepted an appointment as the first president of the Church-owned Marvin College in Waxahachie, Texas, but served for only one year, 1868–9.

Two floors of the Main Building contained the chapel, offices, recitation rooms, laboratory, and library, as well as a book store.