After completing her DPhil at Oxford, Martin returned to Australia to take up a post-doctoral position at Bond University in 1990. However, the unexpected closure of the School of Science and Technology resulted in her leaving Australia in 1991 for a post-doctoral position with Professor John Kuriyan, a structural biologist, at Rockefeller University in New York to work on the disulfide bond forming family of proteins (DSBs) in Escherichia coli. She solved the structure of the DsbA protein which was published in 1993 in the high impact journal Nature.
In 1993 Martin received an ARC Queen Elizabeth II Fellowship. This enabled her to return to Australia and establish the first protein crystallography lab in Queensland. This now operates as the UQ Remote Operation Crystallisation and X-ray Diffraction (UQ ROCX) Facility, of which Martin was the Foundation Director. She remained at the University of Queensland until 2015, supported by several other fellowships: an Australian Research Council (ARC) Senior Research Fellowship in 1999, and a National Health and Medical Research Council (NHMRC) Senior Research Fellowship in 2007. In 2009, Martin was one of just 15 researchers, and only two women, to receive an inaugural ARC Australian Laureate Fellowship. In 2016, Martin was appointed Director of the Eskitis Drug Discovery Institute at Griffith University, which hosts unique drug discovery resources including Compounds Australia and NatureBank
Martin has continued working on DSB proteins and with collaborators developed the first inhibitors of these bacterial proteins as a potential means of combatting antibiotic resistance. She also initiated work on other proteins including phenylethanolamine N-methyl transferase (PNMT), an enzyme that catalyses adrenaline synthesis. Martin published the structure of this enzyme and later, as part of her ongoing research into different PNMT substrate-bound complexes, she and her team became the first remote access user of the Australian Synchrotron. Martin and her team have also contributed significantly to the structural biology of membrane fusion, a fundamentally important process that underpins systems as diverse as neurotransmission and blood glucose control. She wrote an invited commentary for The Conversation in 2013 on this topic, and was invited to present a keynote lecture on her membrane fusion research at the 23rd triennial International Union of Crystallography Congress held in Montreal in 2014. From  2019 to 2022 Martin was Deputy Vice-Chancellor (Research and Innovation) of the University of Wollongong.