Mackintosh's first Antarctic experience was as second officer on Shackleton's "Nimrod" expedition, 1907–1909. Shortly after his arrival in the Antarctic, a shipboard accident destroyed his right eye, and he was sent back to New Zealand. He returned in 1909 to participate in the later stages of the expedition; his will and determination in adversity impressed Shackleton, and led to his Ross Sea party appointment in 1914.