In 1765 he taught during the summer months at Gairney Bridge, receiving about 5s a year in fees and free board in a pupil's home. He became a divinity student at Kinross, with a Scottish sect known as the Burghers, and in the first summer (1766) of his course he was put in charge of a new school at Forest Mill, near Clackmannan, where he led a life marred by poverty, disease and loneliness. There he wrote "Lochleven," a poem inspired by the memories of his childhood, which shows the influence of Thomson. He had already been threatened with consumption, and now became seriously ill. During the winter he returned on foot to his father's house, where he wrote his last and finest poem, "Elegy written in Spring.".Edmund Burke once described Michael Bruce’s Ode to the Cuckoo as “the most beautiful lyric in our language.” ,

As a poet his reputation spread, through sympathy for his early death; and also because of the alleged theft by John Logan of several of his poems. Logan, a fellow-student of Bruce, obtained Bruce's manuscripts from his father, shortly after the poet's death. For the letters, poems, etc., that he allowed to pass out of his hands, Alexander Bruce took no receipt and did not keep any list of the titles. Logan edited in 1770 Poems on Several Occasions, by Michael Bruce, in which the "Ode to the Cuckoo" appeared. In the preface he stated that "to make up a miscellany, some poems written by different authors are inserted." In a collection of his own poems in 1781, Logan printed the "Ode to the Cuckoo" as his own; the friends of Bruce did not challenge its appropriation publicly. In a manuscript Pious Memorials of Portmoak, drawn up by Bruce's friend, David Pearson, Bruce's authorship of the "Ode to the Cuckoo" is emphatically asserted.

This book was in the possession of the Birrell family, and John Birrell, another friend of the poet, adds a testimony to the same effect. Pearson and Birrell also wrote to Dr Robert Anderson while he was publishing his British Poets, pointing out Bruce's claims. Their communications were used by Anderson in the "Life" prefixed to Logan's works in the British Poets (vol. ii. p. 1029). The volume of 1770 had struck Bruce's friends as being incomplete, and his father missed his son's "Gospel Sonnets," which are supposed by the partisans of Bruce against Logan to have been the hymns printed in the 1781 edition of Logan's poems. Logan tried to prevent by law the reprinting of Bruce's poems (see James Mackenzie's Life of Michael Bruce, 1905, chap. xii.), but the book was printed in 1782, 1784, 1796 and 1807.

Dr William McKelvie revived Bruce's claims in Lochleven and Other Poems, by Michael Bruce, with a Life of the Author from Original Sources (1837). Logan's authorship rests on the publication of the poems under his own name, and his reputation as author during his lifetime. His failure to produce the "poem book" of Bruce entrusted to him, and the fact that no copy of the "Ode to the Cuckoo" in his handwriting was known to exist during Bruce's lifetime, make it difficult to relieve him of the charge of plagiarism. John Veitch, in The Feeling for Nature in Scottish Poetry (1887, vol. ii. pp. 89—91), points out that the stanza known to be Logan's addition to this ode is out of keeping with the rest of the poem, and is in the manner of Logan's established compositions, in which there is nothing to suggest the direct simplicity of the little poem on the cuckoo.