In the summer of 1999, 18 families came together with the sole mission of standing firm on the gospel. They sought to have a church that emphasized sound doctrine and the gospel, with the belief that by focusing on Scripture and the absolute truth it contains, fellowship and relationships would grow. It was then that they came up with their motto: "A new light in the Magic Valley."

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After meeting in a backyard for the summer, the small congregation soon realized that they would need a facility and further support in order for their fellowship to continue. With the help of Grace Bible Church in Boise, the group was able to meet at the College of Southern Idaho, led by pastor Jim Harris of Grace Bible Church. By the grace of God, this church had its first service on September 12, 1999. There were over 60 people in attendance that first Sunday, and ministries quickly began.

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By the following year, it was evident that a full-time pastor was needed for MVBC. In March of 2000, Bear Morton came and preached from Ephesians 2, and the congregation excitedly extended the call to him to be their pastor. Bear officially began shepherding the body of MVBC in July that year. From there, the church continued to grow.

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MVBC quickly outgrew its location at the College of Southern Idaho, and they began to meet at First Christian Church in downtown Twin Falls. This became the home of MVBC for ten years, between 2002 and 2012. 

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As the Lord continued to grow His church in Magic Valley, the congregation prayerfully considered finding a more permanent location to call home. The Cain's building in downtown Twin Falls (formerly a tractor repair shop and a furniture store) was a viable option, and by February of 2011, the church began preparations to purchase the building.

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Once the purchase had been made in June of 2011, there was much work that needed to be done in the old furniture store. The location needed to be renovated in order to accommodate a sanctuary, multiple classrooms, and an office space. The congregation quickly picked up the mantle and began demolition, as well as reconstruction. In the meantime, the church met at the Annex in downtown for the regular Sunday service.  

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By the end of March 2012, the old furniture store had been renovated into a church building, and the congregation celebrated Easter in it's new home on Main Street. Work continued on the building as the second floor and lower level needed further attention, but by September that year, the work was finished.

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The ministry continued to grow at MVBC over the next decade, and in May of 2021, the elders of MVBC called their second pastor, Nate Youtzy, to be the new Music Pastor. Ministries had expanded to include a Sunday evening service, a community outreach, a mid-week youth program, and other Bible studies throughout the week.

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The foundation of MVBC, and the motto, is "built on God's Word," and that is the heart of the church. Scripture is clear that the focus of the church must be the preaching of God's Word (2 Timothy 4:2), and that Scripture is foundational to life and godliness for believers (2 Timothy 3:16). Therefore, the mission and purpose remains constant: a light in the Magic Valley which is built on God's Word.