After being called into the ministry, he joined the New York Conference of the Methodist Episcopal Church in 1801 and received his elder's orders from Bishop Francis Asbury in 1805.

In his thirties, Ruter was hired as the first principal of Newmarket Academy in New Hampshire, and in 1821 was offered a professorship of Oriental Literature at Cincinnati College.

In recognition of his contributions to education, Transylvania College, Lexington, Kentucky, awarded Ruter a Doctor of Divinity degree in 1822.

Within a year the Methodist Missionary Society established the Texas Mission, and the bishops appointed Ruter superintendent.

Taking a large supply of bibles, hymnals, and Sunday school books, he headed for Texas in early November with David Ayres as his companion and guide.

Ruter received pledges from several men willing to donate land and he drew up articles of a charter to be presented to the next session of the Texas Congress.

In April, when Ruter attempted a journey to the East to raise money for the mission and to bring his family to Texas, he became ill and was forced to return to Washington-on-the-Brazos.

In 1901, local Methodist leaders, with the support of Bishop Willard Francis Mallalieu, relocated Martin Ruter's remains to Navasota, Texas and erected a granite monument.