In 1891, Macdonald was appointed the Holt Fellow in Physiology at University College, Liverpool, where he did research under Francis Gotch from 1891 to 1897.
After gaining his medical qualifications, he served as house physician at the Liverpool Royal Infirmary for about six months in 1897, under James Barr.
[3] Macdonald's early work was on nerves, initially in collaboration with first Francis Gotch and then Waymouth Reid.
[4]He continued to research this topic at Liverpool, publishing a series of papers in the Journal of Physiology and the Proceedings of the Royal Society.
In around 1908, he began to research the mechanism of contraction in striated muscle, publishing an influential paper on the topic in the Quarterly Journal of Experimental Physiology.
He built a human calorimeter, now in the Wellcome Medical Museum, with which he studied how the heat produced was related to factors such as the intensity of exercise and the subject's weight.