In the fall of 2006, a historic meeting took place in Rochester, New York, where Bishop Gerald West-Phipps, Bishop Benjamin G. Finney, Bishop Rufus McGee, Bishop David J. Singleton, Pastor Robert Livingston, Elder Marcus Hill, and Elder Jerome Livingston gathered to forge a new path for local churches and pastors. Their vision was to create a fellowship that addressed the unique needs of smaller churches, church plants, and mid-sized congregations—needs often overlooked by the national fellowships of the time.

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The brainchild of Bishop Gerald West-Phipps, the fellowship quickly took shape under the leadership of Bishop Benjamin G. Finney, who was appointed as the first Presiding Bishop due to his extensive experience and seniority. Bishop Rufus McGee was named 1st Assistant Presiding Bishop, while Bishop West-Phipps served as 2nd Presiding Bishop. Pastor David Singleton was designated as Bishop Designate, proposed to fill the role of Adjutant Bishop.

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The inaugural Kingdom Dominion Covenant Ministries Fellowship Conference was held in the summer of 2006, drawing over 200 attendees. The event featured a series of classes taught by esteemed instructors, including Bishop Will Compton and Bishop Ronald Hoston. Dr. James L. Cherry Sr. was honored with the title of Bishop for his profound influence on the founders and numerous pastors in Rochester and beyond.

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Following the conference, the fellowship swiftly moved forward, organizing its first picnic, a fellowship trip to Buffalo, and welcoming new members, including Pastor John Young and Pastor Shirley Roberts. In 2007, Bishop Rufus McGee was named Presiding Bishop, and Robert Livingston was elevated to Bishop. However, that year also saw the withdrawal of Bishops West-Phipps and Singleton, leading to a period of inactivity as Bishop McGee's commitments divided his attention.

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Years of dormancy ended in 2012 when Bishop West-Phipps began reorganizing the fellowship. Events were held, and Jerome Livingston was consecrated as Bishop and appointed 1st Assistant Presiding Bishop. The momentum continued into 2016, with the consecration of Bishop Jeremy L. Butler and Bishop Carrie Cox, and the official reorganization of the fellowship under Bishop West-Phipps as the Presiding Bishop.

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With renewed vigor, Bishop West-Phipps appointed executive, national, and other officers to help grow the fellowship. Previous members returned, and new leaders emerged. Bishop Robert L. Livingston became 1st Assistant Presiding Bishop, Bishop David Singleton was named 3rd Presiding Bishop, and Bishop Jeremy L. Butler was designated Intercessory Bishop. The fellowship also welcomed new faces, such as Bishop Owens F. Shepard, Bishop Willie F. Davis, and Bishop Christopher Bryant, who took on significant roles within the organization.

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In 2018, the fellowship experienced a renaissance. Rev. Dr. Jon McReynolds succeeded Bishop James Cherry Sr. as Pastor of Aenon Baptist Church and was consecrated as 2nd Presiding Bishop, providing accountability for the Presiding Bishop. Mother Joyce Rufus was named Mother of the Fellowship, and Libby Swoope became Sacred Arts Coordinator. That year also marked the revival of the fellowship's annual conference, branded as the REFRESHING CONFERENCE, and the introduction of the BISHOP’S ANNUAL BALL & RECEPTION, with Pastor Dwayne Jordan of Albuquerque, New Mexico, serving as the inaugural Gala speaker.

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This fellowship, born from a vision to serve and uplift the local church, has become a beacon of hope and support, continually evolving to meet the needs of its community with steadfast dedication and profound impact.