Duncan Mackenzie was born in Rossshire, Scotland, studied philosophy at Edinburgh University, and received his PhD from Vienna in classical archaeology. After earning a great reputation as a field archaeologist at Phylakopi , he was recommended to Sir Arthur Evans to help him run his dig at Knossos. The two would remain partners in archaeology for the next thirty years.

Mackenzie served as Evans's second in command during his excavations of Knossos. He kept detailed records as Evans's assistant of daily discoveries and served as a middle man between Evans and the inhabitants of Crete. Born to a poor Highland family, Mackenzie proved his capabilities as a talented field-archaeologist. Despite the crucial role he played in the excavations, Mackenzie was eventually fired by Evans. In Time and Chance, Joan Evans said that Mackenzie because very difficult to work during the latter years of his curatorship because of "the gradual onset of his illness." It has also been said that Evans found Mackenzie one night passed out on a table and fired him the next day. However, friends of Mackenzie said that he did not drink. In any case, this removal devastated Mackenzie and exacerbated the mental illness from which he already suffered.

After Mackenzie's death in Italy, some of Evans's system of Minoan dating came into question. It was the meticulous work of Mackenzie that became the key witness in defense of Evans's work. Though conflict existed between Evans and Mackenzie, Evans respected Mackenzie for his contributions to the excavation and paid tribute to his right-hand man in the last volume of The Palace of Minos.