Up until only a few weeks before his death, Macdonald continued to fulfil his calling, travelling the country with the same zeal, and preaching with the same earnestness. His last tour was to the south in September/October 1848. He then preached locally; his last sermon being at Kiltearn Free Church. Macdonald got a blister on his foot which he tended to ignore. The blister got much worse, but by the time he asked the advice of doctors it had got to a stage which could not be arrested. Gangrene set in. The doctors decided not to amputate, just take out the infected part, but the infection had already spread and he died on April 18th 1849.
During this last illness he said to a friend, ‘There are three things which the Lord hath done for me, and may you have cause to praise Him for dealing so with you. He did not expose my heart sins to the world, He did not punish my secret sins in my public work, nor did he alienate from me the affections of His people during all my ministry.’
An interesting story was told by a friend. One day he was close to Ferintosh, so he went to visit his friend, who he found in bed, sick. Sometime during the afternoon Macdonald said to his friend, ‘You have been asking the matter with me; I will tell you now. For some time I thought that God was not revealing Himself to me in His Majesty, as I believed I needed; and I, in my ignorance, was often praying that He would do so. Last Sabbath, on commencing my first prayer in the church, I did so by pleading with the Lord, that He would thus reveal Himself to me; and He was pleased to do so; but the effect was so overpowering to this weak frame of mine that I could scarcely get on with my public duties that day; and here I am suffering in body from obtaining what I then asked.’
A large number of people attended his funeral, and he was buried next to his predecessor, Mr Calder in Urquhart graveyard.