Father Bourgeois was appointed to the Catholic church at Heidelberg in 1851. He travelled on horseback to visit Lilydale, Healesville, Warburton and Yarra Flats about once every two months. A small wooden chapel was built at Lilydale in 1865 which was upgraded to a stone church in 1871. Plans to establish a Roman Catholic Church at Yarra Glen are recorded in 1888 and subsequently St Aloysius opened in Sayle Street in July 1890.

A public meeting was held at Yarra Flats on 12 March 1866 to select a site for a Presbyterian Church. The Bell and Armstrong families who took over Gulf Station in 1856 had travelled to the Kangaroo Ground church each Sunday. With a growing family and other settlers coming to the district, demand grew for a local church. The first building was completed in 1866 and also served as a school room.

From 1879 Methodist services were held at Dixons Creek in the homes of settlers and during the next few years visiting clergymen came from the Healesville or Lilydale Circuits. The community built its own Methodist Church in 1881. Church services were held at Dixons Creek until 1995, although the building had to be replaced several times.

Another Methodist Church was opened at Steels Creek in December 1886. In 1889 the Anglicans opened their building and called it St. Barnabas Church. It was closed about 1959.

A meeting was held at Yarra Flats Hotel in July 1886 to discuss the building of an Episcopalian Church at Yarra Flats. A timber building was erected on the corner of Armstrong Grove and was opened as St Pauls Anglican Church in April 1888. Ten years later the building was moved to a site on the corner of Rudolph Street (now Anzac Avenue) and Bell Street.

The Christmas Hills Anglican community completed their church in 1892. It was built on the eastern side of Ridge Road and withstood bushfires for about ninety years. It was demolished in the early 1990s.

In 1893 Richard Woolcott arranged for a small building to be renovated and placed near the railway station at Tarrawarra to serve as an Anglican church. It was moved to a site on the corner of Old Healesville Road and School Lane in 1901. Services had ceased by 1920 and the building was moved to Healesville in the 1930s.