After joining in an attempt in January 1848 to shorten the hours of labour for millers, Magarey left his position with Ridley at the Hindmarsh flour mill and scoured the outlying areas of Adelaide for work. Two positions provided only short employment and it wasn't until the end of February that he obtained, with a deal of relief, permanent work with James Clark (who later married Ann Craig daughter of James Craig), the recent purchaser of the of the Horseshoe Mill, Noarlunga.

On March 10th., Thomas Magarey married Elizabeth Verco and as he had to commence work the next day he reluctantly left his bride in Adelaide due to unfavourable weather. He wrote in his Diary,

Called in Morphett Vale at the house of brother Greenshields, a brother as yet I had not known. He received me with welcome and obliged me contrary to my intentions to partake of dinner. He then accompanied me to where brother Aird was surveying a spot of ground for a new house for himself. (1)

On March 12., Elizabeth arrived quite unwell, but by Sunday 20th. she had recovered enough for them to attend worship at John Aird's house five miles away. Thomas was much edified by the honest discourse of the excellent brother who spoke.

In this area Thomas and Elizabeth worshipped with the little congregation for about eighteen months. Here he found rich fellowship, harmony and a recovery of his own spiritual life. John Aird was the elder and leader, the congregation consisting of the Watsons, Airds, Greenshields, Browns, Robert Lawries, Magareys and Jones. On December 7th. 1851, two years after the Magareys returned to Hindmarsh, Thomas wrote glowingly of the time spent with John Aird at McLaren Vale where the church proclaimed its restoration teaching but retained the goodwill of the Scotch Baptists among them.

Towards the end of 1849 James Magarey wrote to Thomas his brother asking him to come back to Hindmarsh and take over the mill. The Jacksons had returned to England by mid-1849 and there were only six members present when Philip Messent attended the Franklin Street church in October 1849. The next month Philip Santo, a prominent member of the church, moved to Burra, further depleting the numbers.

On his return Magarey attended a Baptist meeting place in North Adelaide where Captain Scott was the pastor, but he never sought membership. Magarey was asked to bring about a reconciliation in the Franklin Street church which he did, but only after great hesitation due to the fact that he was young and men he had to deal with were those old enough to be his father. So in June 1850 the way was clear for the coming together at Thomas Neill's home in North Terrace and there they re-formed the Franklin Street congregation. Probably as a means of healing the breach, Neill was elected president.

The meeting of reconciliation involved twenty-two persons including - Thomas, Jean & Agnes Neill, James and Ann Verco, George Duke, Joseph & Mrs Penfold, Joseph Hicks, Haines, Mr & Mrs Brock, Johanna Isamann, Smith, Samuel McKay, James Magarey, Thomas & Elizabeth Magarey, Matthew & Betsy Ferguson, Archibald Aird. On June 23rd those chosen for office were:- T.Neill, President. J.Verco, Treasurer. T.Magarey, Secretary.

It was in this year that Magarey paid for the subscriptions of forty copies of the British Millennial Harbinger and distributed them around.

The goldrush of the fifties (in Victoria) denuded the Franklin Street church as well as the colony of its manpower. Thomas often despaired of the situation and wrote,

we have no good public speakers in Adelaide. Brother Aird can labour well among the Scotch, but it is not so intelligible to an English audience; besides his station is in the country. For myself, the only way I can be useful is in circulating the printed thoughts of others. (2)

It is here in the same letter to James Wallis that he castigates the Scotch Baptists, calling them a self-righteous people with their predestinarian notions and claiming he would never waste his time on such an obdurate people if he could have his time over again.

By the end of 1852 Magarey hoped for a change in the church situation.

As a church we have with difficulty (occasioned by the absence of our brethren at the goldfields) dragged through our existence to the present time, after having scarcely enough male members to conduct the worship; but...our brethren are gradually returning. (3)

In March of 1853 he stated that the demand for labour in Victoria was still very great and in June of the same year he wrote that the condition of the church was still no better. Near the end of 1854 though, there was an influx of immersed believers from another church, This considerably increased the congregation and made the work of the church much easier.

On November 5th. 1854, Magarey offered his building in Hindmarsh for worship. This was accepted and on June 3rd. 1855 he indicated to the members of the Franklin Street church that those members residing at Hindmarsh intended to form a church.

But ill-feeling arose (at the decision to form a church at Hindmarsh).. Instead of this being received with joy as a token of the Lord's goodness, to my astonishment it was received with a storm of innuendo and disapproval...(4)

In December 1855 a meeting of the Franklin Street congregation was held to consider building a new chapel. Before he left Adelaide on an overseas trip Magarey left £400 with Henry Hussey to be used in building a new chapel in Grote Street, on condition that the church raise £800 and paid off the total debt in three years. (To his disappointment the debt was not paid off for many years.) J.Verco offered land in Grote Street for £300. This was accepted.

The Grote Street building was opened in December 1856, but in May of the following year a major dispute arose in the congregation over the appointment of pastors. The issue was forced and pastors were appointed with the result that those who had signed a protest document (22, including Hussey the Secretary and Armour the Treasurer) along with others left the church and joined Captain Scott's Baptist church in North Adelaide.

The Magarey family in 1857 went to live in Enfield, where Thomas had purchased about 60 acres of land and built a handsome three-storeyed home, with a flat roof, on which he installed a telescope for the study of the stars. It was a long way from Enfield to worship at Hindmarsh, but the family went there regularly until 1868 when they left to become foundation members of a church formed in Whites Rooms. Hindmarsh was a very large church then of about 300 members.

A visit from a distinguished Disciple in Scotland, Thomas Hughes Milner, gave the churches in Australia an awakening. Milner had come to Melbourne for a rest and to inspect some property owned by his wife. Prevailed upon to preach he sparked off a period of intense evangelism. Magarey spoke of Milner

as a man of education and considerable power as a preacher. Moreover, he really loved the Lord Jesus Christ. I felt there was something earnest end real about him and felt encouraged. (5)

The churches were doing very little in those days in the way of evangelism, concentrating mainly on what they thought as being correct in church practice. Magarey had subscribed annually to the Evangelists' Fund in England, but was greatly disheartened that they were doing very little in the way of evangelism.

Milner took the view, and this was also Magarey's view, that Australians should do something for the country they lived in. At the time it seemed difficult t o stir the churches, but action could be taken by individuals. Milner promised to try and send out a suitable man and recommended a man named Evans, but he never came. Magarey was, however, in touch with James Wallis concerning an evangelist and Wallis read the letter to a young evangelist Henry S.Earl from America who was at that time in England the country of his birth.

Earl declined the invitation, but being pressed by Andrew Thomson of Melbourne with whom Magarey had discussed the matter of an evangelist, decided after all to come to Australia arriving via the United States in 1864. In Melbourne it was soon found he had a great capacity f or preaching and drew great crowds.

For a long time Magarey had been writing to America and England requesting an evangelist be sent to South Australia and he was deepIy disappointed that the members of Victoria had decided to go it alone . Going over to Melbourne he heard the eloquent evangelist and saw at once the power of the Gospel he preached. Thomas remarked,

He had great and unparalleled success in making converts and baptising, which at once stirred up evil feelings of jealousy among the old stagers who had been set aside, and the old church members who were overwhelmed by the converts. (6)

In Adelaide, Earl’s preaching brought great additions to the Hindmarsh and Grote Street churches. The next year, March 1865, at a welcome in Adelaide for Earl and T. J .Gore, Earl stated his approach to preaching. A report of the meeting included the following.

His purpose in coming among them was simply to preach Christ and him crucified, Christ and him raised, Christ and him glorified, and Christ as the only Being who had the right to rule, guide, and control the hearts of men. It was not to build up any sect or party, but maintain as far as in him lay the truth as proclaimed by the Lord and his apostles. (7)

The "New Town Hall" was packed to capacity with many unable to gain admittance.

Thomas Jefferson Gore who had studied at the College of the Bible, Lexington, Kentucky, arrived in Adelaide with Earl in 1865, and all looked well for a great future the South Australian churches. Gore was at first eagerly welcomed but as time went by many of the old stagers began to show resistance to his American approach. The leadership of the Grote Street church was divided over the authority of the evangelist and that of the elders. (In Britain evangelists were subordinate to the eldership; in America the minister or elder, as he was then called, assumed greater powers of leadership. (8)

James C.Verco and W.H.Burford, elders at Grote Street, and Philip Messent and T.S.Lyle, deacons, were some who broke away and established themselves as a church in Kermode Street, North Adelaide. Philip Santo, the leading elder of Grote Street followed the American thrust and went with Gore and Earl. (Gore married two of Santo's daughters, the second after the first died, and family ties probably helped his decision in some way.)

Within two and a half years of Gore's arrival the Grote Street church was extinct, Magarey buying the building to salvage something of what was once the focal point of the restoration movement in South Australia.

Earl opened the Hindmarsh chapel in 1866, worked with the church for a period of time during 1857-68, then formed a church in Whites Rooms on October 25th (because of the dispute over leadership), the responsibility of the congregation being taken over by Gore at the beginning of 1870 for the period Earl was in New Zealand. On Earl's return Gore and Thomas Porter commenced a church at Norwood in March 1871, Philip Santo delivering the inaugural address. Magarey and family joined in membership with Earl at Whites Rooms, probably to show his support for the American evangelists. (Earl had earlier married Thomas' niece, Anna Magarey, a daughter of James Magarey by his second marriage.)

Early in 1873 the Grote Street chapel was again in the hands of the city congregation, re-opening for worship on July 6th with T. J.Gore as evangelist.

One of Magarey's visions was the establishment of a Bible College for the training of young men for the ministry. It was at first proposed by G. F. Angas to unite with the Baptists and set up an undenominational college, but after some consultations between Messrs Angas, Stonehouse and Mead (Baptists), and Earl, Gore and Thomas Magarey, (Disciples), the Baptists told Mr Angas they would not have anything to do with the Disciples. Henry Earl then decided he would go to America to raise funds for the Bible College and suggested Alick Magarey, Thomas' son go with him. Magarey offered £4,000 for the fund if the churches gave a similar amount. The appeal was only a partial success, not enough to operate a full-time college. Later other small sums arrived from England and America, but the fund was largely ignored by the Australian churches much to Magarey's bitter disappointment. As Magarey's generous offer was never taken up the idea of setting up a college in South Australia lapsed.

A project dear to Magarey's heart was the commencement of a periodical the Australian Christian Pioneer in 1868, Earl and Gore were to be the editors but as Earl was not regarded as a writer, Gore and Magarey shared the responsibilities of editing, although as Thomas says,

Gore was the real editor, and I was the treasurer to make good all the deficiencies, and they were many. (9)

Magarey was a proponent of the restoration movement in Churches of Christ for 35 years, but after struggling for some time with personal disappointments with people and the churches, he was attracted to the significance of the new birth resulting in he and his wife joining the Brethren, August 29th. 1880.