The Lochs free Church was formed in 1843 as a result of the Disruption in the national church. The national church had previously been in the area of Keose, which was a central point in the Lochs area given that much of the travel was undertaken in boats. The newly formed church was located in Crossbost and originally continued to serve the whole of the Lochs area. Many members of the congregation sailed from Cromore, coming from villages further afield such as Marvig and Lemreway. Cromore, at the time, was the only village with a pier and proved to be a key point in the travelling of the members and adherents of the newly formed church from the south Lochs area.

The first minister of the Lochs Free Church was the Rev Robert Finlayson, who had resigned from his charge from the national church in Keose following the disruption. Rev Finlayson spent the first two years living in Stornoway whilst the manse was being constructed. The first free church and manse in Crossbost were built in 1845, however the current building which stands today was rebuilt in 1892. The final piece of the rebuild was a hand carved dove, which the builder created using a block of wood and a penknife, this was placed above the pulpit and remains there to this day.

In 1849, the Finlaysons experienced a tragic accident which took place not far from their manse at Crossbost. Two of their sons, Donald, aged 17, and Robert, aged 14, accompanied an old sailor in a boat in the loch, and although it was a hot and fine day, all were drowned. Rev Finlayson preached the following Sabbath day as usual, despite the funerals not yet having taken place. Rev Finlayson left the congregation in 1856 to take up post in Helmsdale, he passed away in 1861.

By 1870s the people of south Lochs were beginning to become weary of the travelling to and from Crossbost. This resulted in a campaign to form a Free Church to serve the area of south Lochs. In 1880 the residents of south Lochs saw their campaign come to a successful end with the formation of their own congregation in the local area. Following similar campaigning in the Kinloch area, a Free Church congregation was established there around the same time and thereafter, despite the permanent retention of the title 'Lochs Free Church', the congregation served the North Lochs area only.

North Uist born, Rev John MacDougall, who had been ordained into the Lochs Free Church in 1885 having elected to go into the union of 1900, remained in the church building until 1904. Following a lengthy court dispute in which the House of Lords ruled in favour of the traditional Free Church's ownership of the buildings over the newly formed United Free Church's claim. But in spite of this ruling, the Free Church gained their buildings, but only 29 ministers in Scotland elected to stay with the Free Church, with the majority going with the United Free Church. Interestingly, the only minister on Lewis to stay with the Free Church was Rev Hector Cameron who had been the minister of the Lochs Free Church from 1876 until 1881.

Despite Rev MacDougall's move to the United Free Church, the majority of the congregation had remained faithful to the Free Church and were back in the church building by 1904. However the lack of available ministers meant that the position was vacant until 1909, when Rev John Rose, a Gaelic speaking Scotsman, took up the position having previously been the minister of a congregation in Nova Scotia.

In the 1920s, meeting houses were erected in each of the villages in the north Lochs area: Achmore, Crossbost, Grimshader, Leurbost and Ranish. These were originally intended to be used as a centralised meeting point for the villages, however these became almost exclusively used for hosting the mid week Gaelic prayer meetings. In the late 1990s, English prayer meetings were introduced for the first time. Each meeting house held a prayer meeting in English once a month on different weeks. This allowed the non-Gaelic speaking members of the congregation to attend a weekly prayer meeting, albeit with a bit of extra travelling involved.

The manse, which had stood since 1845, was demolished in 1977 following the completion of the new manse, which is still used today. The stone from the demolished building was kept within the local community and was used in the construction of the new pier in Crossbost, located beside the Free Church.

A new hall at the church was completed in 2000. With the new facility set up, the mid week prayer meetings were unified from the fragmented meeting houses and moved to the central position of the church hall. The last of the localised mid week prayer meetings took place in 2004. As the meeting houses were never feued, and as a result couldn't be sold, they were returned to the owners of the crofts they had been built upon.

In April 2016, the church formally announced that the regular Gaelic services would cease. This was a sign of the changing times with many of the Lochs natives not being fluent Gaelic speakers, declining numbers attending the Gaelic services and the continued difficulty of sourcing ministers who could preach in the language.

In March 2020, due to the global pandemic resulting from the spread of COVID-19/Coronavirus, the church took the necessary step of shutting it's doors in order to protect the attendees. However, this took the church into a new era as live streams were started and the Sunday sermons were broadcast through the YouTube platform and the prayer meeting was able to continue using the Jitsi video conferencing service.

The church reopened it's doors on the 8th November 2020 with numbers being restricted to fifty and two meter social distancing enforced. However further limitations were also in place to avoid the virus spreading including the use of face masks and sanitiser. The singing of praise items was also prohibited under the government guidelines and these were limited to morning services, with the evening service being available for streaming online.

Whilst the island had not been hugely affected with cases of COVID-19, localised outbreaks of the virus caused the Western Isles to be moved into Tier-4 restrictions, the highest level, which resulted in the church once again closing it's doors on 29th January 2021. Following a drop in cases and the successful roll out of the vaccines, the church was able to open it's doors once again on the 28th March 2021, with the previous restrictions in place and again for the Sunday morning services only.

With restrictions starting to ease, the church was able to re-commence items of praise in June 2021, however the necessity to continue wearing face covering meant that the praise was limited to two psalms: one at the beginning and the other at the conclusion of the service. With infections falling and the number of people being vaccinated reaching 75%, national restrictions were further relaxed and the need for social distancing was removed and people were free to sit in their pews of choice on Sunday 15th August 2021.

•     Rev Robert Finlayson, 1843-1856

•     Rev John 'Big' McRae, 1857-1864

•     Rev George. L. Campbell, 1865-1875

•     Rev Hector Cameron, 1876-1881

•     Rev John MacDougall, 1885 -1900

•     Rev John Rose 1909-1919

•     Rev Malcolm Maciver 1924-1959

•     Rev Donald Gilles 1960-1982

•     Rev Kenneth Ferguson 1984-2000

•     Rev Alasdair Macleod 2003-2011

•     Rev Calum Iain Macleod 2013-present