John Malcomson was born in Keith in 1802, the same year as Hugh Miller, but moved with his mother to Forres after his father was lost at sea in 1806.

From 1816 to 1818 John Malcolmson obtained a bursary to King's College, Aberdeen, where he studied mathematics, chemistry and natural history. In 1819 he matriculated at Edinburgh University where he studied medicine, graduating in 1822.

On 9th May 1823 he was appointed Assistant Surgeon in Madras. He served first with the 45th Regiment of Native Infantry at Arni and Jalna, from June 1824 until August 1825. During this time he wrote the Common Place Book. In May 1825 he published his first article in the Bombay Courier, and this encouraged him to continue his writing.

In September 1825 he transferred to the 3rd Light Cavalry, and continued to write, and in 1831 graduated from the columns of colonial newspapers to "Prinsep's Journal", where he published an article "On a remarkable aerolite." This was followed by articles in other journals which mark the beginning of his interest in geology.

He was eventually appointed Secretary of the Madras Medical Board in 1834 and returned home for a few years in 1836 with a large collection of fossils from the Nummulite Limestones along the Nile. Whilst at home he was promoted to Surgeon in the East India Company's service.

Malcolmson's work to establish the correct geological sequence of early sandstones in the Moray Firth was concentrated into a few months in 1838 working together with local amateur geologists. On a national level he was highly regarded by Hugh Miller and Charles Darwin. Darwin refers to Malcolmson in the "Voyage of the Beagle" and also in "Structure and Distribution of Coral Reefs".

After graduating MD at Edinburgh University in 1839 he again returned to India in 1840 where he continued his geological research. In 1842 he was appointed Secretary to the Bombay branch of the Royal Asiatic Society and in 1843 made an expedition to map the osseous formation and explored far into the interior starting from Surat to the north of Bombay. Malcolmson died during a second expedition ot the area in 1844 near Dhulia.

Fossils and minerals which had been left at his mothers home, Cluny Cottage in Forres (which he had built for her) were presented to The Falconer Museum in 1859.