After early literary ventures and a six-year period as a bank accountant in Cromarty, Miller went to Edinburgh in 1840 as editor of the newly founded newspaper The Witness. The newspaper, which opposed patronage in the Church of Scotland, gained a wide reputation through Miller's leading articles. He also wrote a brilliant geological series for it, part of which was published in book form as The Old Red Sandstone (1841). In this work he described his discoveries, in Cromarty, of fossils found in formations of the Devonian strata (approximately 415 million to 360 million years ago).

Of his remaining works on geology, Footprints of the Creator (1849) was the most nearly original. The book recorded Miller's reconstruction of the extinct fishes he had discovered in the Old Red Sandstone and contended, on theological grounds, that their perfection of development disproved the theory of evolution. He also discovered the fish species subsequently known as Pterichthyodes milleri. It was largely from Miller's writings that the Devonian Period became known as the Age of Fishes.