In January, 1804, Wilson returned to St Edmund Hall as a tutor and by January, 1807, had been appointed vice-principal. He combined these positions with charge of the parish of Worton, between Banbury and Woodstock, which was in his uncle's gift. We have emphasised Wilson's standing in the evangelical succession and as Loane suggests one might have expected 'useful service comparable to that of Charles Simeon in the sister seat of learning'. 'But' observes Loane 'Wilson was neither fitted by nature nor suited by office to do for Oxford the work which Simeon had done for Cambridge' – not being rector of a church or fellow of a college at first.
He did say before going there
I fear Oxford. I tremble to think of its Dons, and its duties, and the general tone and colouring of its maxims and opinions. I cannot forget the past. I cannot but dread to encounter new trials, new men, new pursuits, with a variety of difficulties and temptations hitherto unknown, unheard, unthought of. But to shrink, would prove me faithless. I undertake the office, not of my own will, but from a sense of duty.
Oxford was not a complete failure. He was asked to preach before the University in January, 1810. However, it did take its toll on him inwardly. Already in 1804 he is writing
I like my position. Everything falls out as I could wish. But I see many dangers looming in the distance. My heart is already becoming entangled in worldly studies, so that divine things lose their savour. I wish to count all things loss for Christ. I wish to love and cherish divine concerns; but pride, ambition, secular pursuits, and cares, beset me and make my path slippery and insecure. Pray for me.
Two years later it is
My soul is sick. I am perplexed and overborne with college and university business. I have wandered from God. You would not believe, my friend, how weak my mind is, how perturbed, not to say hardened, so that I feel no love for sacred things, nor derive any profit from them. Sin, disguising itself in the form of those literary pursuits in which I am engaged, has deceived, wounded, and almost slain me. I scarcely see Christ, and scarcely love Him. That glow and fervour which I used to feel spreading over my whole soul, is extinguished. Well do I know that I have grieved the Holy Spirit.
Then in 1807 he laid aside his journal not to take it up again for over 20 years. By 1809 he was convinced of the need for a return to pastoral ministry.
The employment of a tutor at Oxford has been far from being perfectly congenial to my mind. As to the propriety of my leaving the university, and giving myself wholly to my ministry, I cannot have a doubt. The gradual decay of vital piety in my own heart, is too obvious and too alarming a symptom, not to force itself upon my conscience. May God yet spare me for His honour!
He summed up much later
My time at Oxford was utterly without profit as to my soul. Pride grew more and more, and carnal appetites enchained me. On the other hand, Worton afforded me much spiritual consolation. These nine years were passed, I trust, in the path of duty, though amidst struggles, temptations, and frequent estrangements of soul and spirit.
Worton had been the one bright spot in this time of dearth and he had ministered faithfully there until he began, from 1808, to assist Cecil at St John's Chapel, Bedford Row, Bloomsbury, London. In June 1812 he took full charge there, resigning his Oxford posts and moving to London. Begun as a Chapel of Ease in the reign of Queen Anne, St John's was seen as the headquarters of London's evangelical party and Wilson was an obvious choice.
There he devoted himself to 'ceaseless activity' as a powerful, forthright and popular preacher. Loane speaks of his 'commanding oratory' and of 'years of great blessing' noting how, having preached only 640 sermons in the 11 years of ministry before Bedford Row, he now preached 1187 sermons in just 15 years! His 2000 strong congregation of 'lawyers and merchants', swollen by other visitors in the season, was peppered with Wilberforces, Macaulays, Thorntons and Grants of Clapham Sect fame. Very diligent in preparation, he would take only a few notes with him into the pulpit. Loane says
He stood as God's servant to do God's work and his power was soon felt by all. He was in earnest at a time when earnest men were still comparatively hard to find; he preached a full gospel in an age when preachers of the gospel were few and far between. He was steadfast where many were given to change, and moderate when others ran to extremes. His grave and dignified bearing was a solemn rebuke to the spirit of levity or unbelief, and his impassioned address to conscience was varied with an impressive pathos of appeal.
In 1821 Wilson took the funeral of commentator Thomas Scott. He was always a fan of Scott. He describes their last interview in 1819 thus:
I sat up with Mr Scott last night till near 12 O'clock, talking over my correspondence with the Bishop of Chester on the doctrine of salvation. This morning he gave us a most beautiful exposition of Romans 10. 12, &c. Afterwards Mr Scott went over my homily sermon with me. He alters but very little, and approves of most of my ecclesiastical notions. Mr Scott is tolerable in health, though 72 years old, and asthmatical for 45 years. He is very busy with his new edition of the Commentary on the Bible. He has now finished the whole of the first volume, and parts of the second and third. He finishes four or five sheets a week, expounds twice a day, has above a hundred communicants at his sacrament, is popular and beloved in his neighbourhood, and has fuller churches than ever. It is quite delightful to see him once more in the flesh.
Scott was someone he always delighted to honour.
There was no one in whom he placed more confidence, no one whose writings he more habitually studied. To the close of his life, Scott's Commentary on the Bible was the book of his choice. It exactly suited him. He never seemed sensible of its defects. He never felt it heavy. New authorities arose, new comments appeared : but still his word remained the same - "The old is better." He recommended it to every one whom he valued, and read it always himself. Its accordance with Scripture, its perfect honesty and integrity of purpose, its moderation in statements of doctrine, the practical and holy tendency everywhere manifest; all these won his heart and kept it.
He used Scott's commentary with his Bible daily. He never passed a copy, however old the edition, without buying it. At one point he began having it translated into French. When his two sermons on Scott were published some thought his praise too great.
“Thomas Scott was a wonderful man" he used to say, "as wonderful in his way as Milton or Burke. He overcame great difficulties, and lived down great unpopularity. Why, he was at first quite hooted in London for his long sermons."