Founded in 1906, the present church building was completed 1910.

In 1905, with John Hartman as spokesperson, a group of these Catholics approached Archbishop Moeller with a request that a priest be sent to celebrate Mass in Batavia.  After being informed that no priest was available to make trips to Batavia on Sundays. they contacted Fr. Chrysostom Theobald, Provincial of the Franciscan Order, who promised to send a Franciscan priest to offer Mass if the Archbishop approved. Archbishop Moeller granted permission contingent on the people making all the preparations. They obtained the use of the John Klein Building on Main Street with free rent for one year, and on March 11, 1906, the first Mass was celebrated in Batavia by Fr. Chrysostom Theobald. The Franciscans continued to offer Mass there on an average of twice a month until 1910 when the new church was dedicated.

In the 1920’s the parish grew to 60 families. Decisions were made to improve and expand the parish facilities. With the parish growing, it was determined that a pastor would be sent to reside in Batavia. In 1952, the house adjacent to the church on Sixth Street was purchased for the sum of $8500 and was remodeled to serve as the parish rectory. In the same year the interior of the church was also renovated.  Additional renovations and additions were made from 1960's to the 1990's.  In 2006, the church celebrated its centennial -- 100 years of faith in the community.  

On July 1, 2012, the four parish region of Holy Trinity, St. Ann, St. Louis, and St. Philomena were gathered together under the name of Clermont Catholic Communities. The overseer of this process and the pastor of this new four-parish region was Father Jerry Hiland, who up until that time had been pastor of St. Louis and St. Philomena.  Father Martin Bachman was assigned to the parish region in 2015, and in 2022, Father Thomas McCarthy was named pastor of this parish region, now known as Beacons of Light SE-5 or Holy Family Parishes.