After several years of much labour and perseverance, attended with their certain - though often apparently dilatory - reward, Mr Thomas was called to suffer most acutely both in body and in mind. In 1827, a painful division took place in his church which resulted in the formation of a second Baptist church in the town, one that continues to this day. And in the following year he had to undergo another kind of suffering which was not less tolerable. Mr Thomas wrote of it like this "From the 18th of Feby till the 22nd of March I was from home in London undergoing a great & severe operation, viz, the removal of a Tumour weighing Six Pounds & one ounce from my left knee". When Mr Thomas returned to his much loved work and people, he did so with a deeper sense of the mortality of man than ever, as well as with a heart full of thankfulness - as appears from the texts he preached from at the time. See 1 Corinthians 15:31 and Psalm 92:1, 2.
In 1836, Mr Thomas's connection with the college came to a close, mainly because of his health which had become so precarious as to prove a serious inconvenience.
In 1845, under June 1, after preaching from 1 Peter 2:24, Mr Thomas writes "This was the last sermon preached for fifteen weeks, the longest time without preaching in 43 years. The most dire attack and scene of personal affliction prevented my engaging in my long accustomed work for so many weeks. My recovery was the wonder of all around me. Bless the Lord, O my soul! Psalm 103:1-5." And at the end of the same year he notes "Thus ends another in the summer of which the writer was wonderfully restored to health." It is of the Lord's mercies that we are not consumed, because his compassions fail not Lam 3:22.
Mr Thomas' final years were spent in comparative privacy. In 1843, however, he preached the annual sermon in connection with the college where he had been president; and in 1846 he did the same on behalf of the college where he had been a student. He spent the evening of his life in the serving of his own flock; and in the very midst of his work, and with unimpaired mental abilities he was taken to his reward. Only one Sabbath intervened between his occupancy of the pulpit and his departure, and on the Monday evening preceding hsifatal attack he led the devotions of his people in their socil meeting for prayer.
What an unusually solemn day it would have been on the 20th of November, 1853, for the worshippers in Frogmore Street, had they known that that Sunday was the last for them to see their beloved pastor, who had ministered to them in holy thinhs for nearly 47 years in their pulpit! Had some friendly angel gently whispered this much to them that morning - would not they have looked downcast! Solemn! Yea woukd they not have been all attention while the servant of God was addressing them for the lat time, as his feet stood on the edge of that river which he was about to cross?
Few, perhaps if any, thought, when he read his text that evening, that that was the las, and indeed there was something solemn and appropriate in the verse taken, Behold, I come quickly: hold that fast which thou hast, that no man take thy crown. Rev 3:11. Mr Thomas preached that evening with unusual energy and effect. The vigour of youth and the mellow piety of old age had met so that his soul was most happy in his work. That service being over, his work on earth was done!