The Society for Propagating Christian Knowledge obtained for him an invitation from the Gaelic Church in Edinburgh, where he went in January 1807. His father came to help him move, and as they left his humble cottage, while a storm was raging, the roof of the cottage was blown off. His father said, ‘John, I think it was high time to leave Berriedale.’
His charge in Edinburgh was very different to what he had been used to. His natural affability made him a good pastor. He had a difficult task as his congregation came from all over the Highlands, and many had lost their initial Christian fervour due to embracing things of the world in the big city. However, he was able to knit them together. He gave two Gaelic sermons, an English sermon in the evening; there were regular prayer meetings, district catechising and a weekly lecture. He would regularly visit his people in their homes, so that he could build up a relationship with them. On one occasion he visited a woman whose husband was a Catholic. The husband was supposedly dying, having been instructed not to eat anything by his priest who had administered extreme unction. Macdonald spoke to him, persuading him to eat something as he was very thin. As he was eating the priest arrived; he was furious and tried to snatch the food away, but Macdonald stood in his path. The priest sullenly withdrew; the man recovered, attending the Gaelic Church from then on. Macdonald took advantage of the learned men that he met during his time in Edinburgh, taking in what they said and carefully studying the books they commented on.
During his time in Edinburgh there is strong evidence that Macdonald experienced a second baptism of the Holy Spirit. This was very evident in his preaching. Always clear and sound in his statements of objective truth, his reaching now became full of life. It was now searching and fervent, as well as sound and lucid. He warned sinners which excited the wonder and awe of his hearers. His statements of Gospel truth were from one who deeply felt its power. People could tell that he spoke from his hearts to theirs. His manner in the pulpit changes as well, becoming more vehement. His sermons, always full of thought, bright with illustration, and teeming with feeling, were delivered with the most unaffected and intense earnestness. Many noticed the incredible change in his preaching.
Soon afterwards he went to see his father in Caithness; on the way he was asked to preach by the minister at Tain. In the congregation was a man who had walked sixteen miles. “When the sermon began I forgot all but the doctrine I was hearing. As he warmed up with his subject, the preacher became most vehement in his action; every eye was rivetted on the speaker, and suppressed sounds testified to the effect which his sermon was producing. His second discourse was so awe-inspiring that the audience became powerfully affected. Such was the awful solemnity of the doctrine and the vehemence of the preacher's manner that I expected, ere he was done, every heart would be pierced, and that the very roof of the church would be rent. The sermon over, all were asking who the preacher was. 'A young man from Edinburgh of the name of Macdonald,' was the only answer that could be given."
On September 1st 1813 Macdonald became the minister at Urquhart. His predecessor was the eminent and godly Charles Calder, who did much good work in the parish and who was much loved. It was a well run and gifted parish, where virtually every parishioner attended church. Because it was in such a good condition Macdonald did not have to spend all his time building up the parish, so he could spend a good deal of time elsewhere. Sometimes when he had been away for six weeks, there would be murmurings of complaint, but as soon as they heard his preaching and were greeted by his smile; the murmuring was forgotten.
The Gaelic Church is marked 'b' on the 1805 map. The map can be seen online at the National Library of Scotland website. The road layout has changed, so I estimate that it was in the middle of Johnston Terrace.