The church started as a result of a Bible study. God was working in the hearts of a group of people who attended a Bible Conference in Glenn Eyrie, Colorado. Upon returning from the conference, they were informed that their Pastor would be transferred. It was rumored that a lady might assume the Pastorate. A group of people in the church continued their study of what the Bible taught and presented their beliefs and concerns to the District superintendent. The group was informed that the situation would not change. 

After much soul-searching, people decided they could not, in good conscience, stay at the church. The decision was not made as a group, but rather made individually through careful study of God's Word. Without a church home, many people found themselves looking for a place to worship the following Sunday. A small group would meet on Sunday Morning for Sunday School. After Sunday School, the people would go to various churches in the area and meet later to discuss what they had learned. Others in the community were also involved in searching for a church home at this time—these people, on their own and as a small group, were now looking for a place of worship.

The church of Christ in Holly Springs closed in April of 1989, sat empty, and was eventually offered as a place to meet. By this time, God had impressed 2 issues upon this group. One was the importance of God's Word being preached freely and without a mandate from an organization. The other was the importance of community, and especially the need for Fellowship. It was a consensus that something had to be done within the community. It was decided that an open meeting would be held in the Church in Holly Springs on the first Sunday night in November 1990. Many people from the community attended. It was an exciting and very emotional evening. The night included prayer and encouragement, and it closed with Amazing Grace.

There were several meetings over the next 2 weeks. A name was determined with the children's help. The order of service, along with the music and other details, was determined. Washington Heights Chapel in Sioux City had promised to help in any way possible. Pastor Dan Speichinger (Washington Heights) was asked to speak because of his key role in encouraging the Fellowship. On November 18, 1990, God allowed a church to start in this community. Approximately 35–40 people were in attendance. It was a tremendous joy to see God work in the services.

Over the next few months, various speakers would come each week to fill the pulpit. A church Board was formed, and in June of 1991, a young college student (Jim Penner) at Grace University was hired on a part-time basis to help at the church. In May of 1992 Dr Wes Hansen helped the church for a few months. It was during that month that many people came to know Christ as Savior. Pastor Wes helped clarify and solidify the church's doctrinal statement. God amazingly used him in just a few short weeks. The board asked Wes to preach for another month, but he had made other plans. He recommended his former Youth Pastor, Jim Thomas.

Jim Thomas was contacted and preached for the first time on June 7, 1992. He was asked to preach again, but could not for the next 2 weeks due to other preaching engagements in South Dakota. Jim and his wife were canidating at a church in Canton, South Dakota. He and his wife met with the board in South Dakota, and were being considered to come on as a Youth Pastor and then take over the Pastorate when the Senior Pastor retired in the summer of 1993. Over the following weeks, Jim began filling in at the pulpit at this church. Pastor Jim had to decide on the church in South Dakota, even though there was no commitment from the board or Pastor Jim to the Holly Springs Fellowship. He decided to turn down the Church in South Dakota. In the summer of 1992, Jim was asked to stay on as a part-time Pastor until the end of the year. He agreed, and through a series of unusual circumstances, he and the board realized that this was where God wanted him. In November, a place to live was found, and work began on getting it ready. In December of 1992, he came as the Pastor of Holly Springs Bible Fellowship. In April of 1993, he became a part of the community and moved into the area. He continued as a bi-vocational Pastor for about 10 years. He presently serves as the Senior Pastor of the church.

Following the 1998 floods in Holy Springs, the church built a new building in 1999. A second debt-free building was built in 2017. All the work on the buildings has been done by the people in this Fellowship, and the buildings were built debt-free without fundraising or Capital campaigns. 

As a result of numerous prayers and through a series of unusual circumstances, God brought Jimmy and Sara Cockburn into our Fellowship. In 2021, Jimmy was brought onto the staff of Holly Springs and is part of our succession ministry to lead Holly Springs Bible into the future. 

This Fellowship has been the result of the prayers of many saints over the years. What has been accomplished in this community is the result of God's hand. Credit cannot go to anyone other than our God, because anything accomplished is only through Him. We are excited that God has allowed us to be part of his wonderful plan and look forward to being part of what God does in the future.