Fellowship Baptist Church of Harmony Grove was started as missions project of the Wisconsin Fellowship of Baptist Churches at the request of some Lodi area families in 1989 and the church was formally incorporated in 1990. The WFBC director, Leon Leeds, was the 1st pastor, serving as Paul to a young Bob Jones University Graduate, John Roth, who became the 2nd pastor in 1991, serving in that capacity until 2006 when he resigned.

The assembly 1st met in the old Lodi High School, moving to what is now the Hometown Community Bank building in Harmony Grove after a few weeks. The church moved to the Arlington Prairie Lutheran Church in 1992, bought land in Harmony Grove in 1994, and began construction on the current church building in 1996, meeting there for the 1st time in October of that year.

After Brother Roth's resignation, a pastor search committiee offered the job to Eric Hafeli, a Hyles Anderson graduate, in February 2007. In January, 2022, Pastor Hafeli announced his retirement.

At its peak in 2005, attendance averaged 55 for a Sunday morning service. For the past 2 years, it has averaged 17-18. The church has had an unusual number of families who attended, loved the church, but moved away for family or work reasons, especially in the last 10 years.

Most of the current attendees are 55 or older. There are a couple of families with teens. The church corporate owns the building. Last year was the 1st in a few years that income ran below expenses.

Originally, the pastor was a part-time position. Around 2002, the pastor's position was changed to full-time, though he is an independent contractor. The pastor's total compensation for 2021 included a housing allowance, an auto allowance, salary, and a monthly payment towards health insurance totaling just under $49,000. Compensation for the new pastor is unknown at this moment, but is estimated to be $30-40,000 depending on time commitment.