In addition to the research fellowships awarded during her career, Martin has received many honours in recognition of her professional contributions including:
*2005 Roche Medal, Australian Society for Biochemistry and Molecular Biology
*2005 Queensland Government Smart Women Smart State Award (Research Scientist Category)
*2006 Women in Biotech Outstanding Biotechnology Researcher Award
*2007 Dorothy Hodgkin Memorial Lecture, Oxford
*2007 Honorary Life Membership, Questacon (National Science and Technology Centre), Canberra
*2010 Lady Masson Lecture, The University of Melbourne
*2011 Women in Technology Outstanding Biotechnology Achievement
*2015 Finalist, Newscorp QLD Pride of Australia Inspiration Category
*2015 Finalist, NAB Women's Agenda, Mentor of the Year
*2016, Finalist, Queensland Telstra Business Women of the Year, Public Sector and Academia
*2017, Wunderly Oration and Medal, Thoracic Society of Australia and New Zealand
*2017, Elected Fellow of the Australian Academy of Science
*2017, Elected Eminent Fellow of the Royal Australian Chemical Institute 
*2017, Inducted Bragg Member, Royal Institution of Australia
*2018, Made a Companion of the Order of Australia for "eminent service to science, and to scientific research, particularly in the field of biochemistry and protein crystallography applied to drug-resistant bacteria, as a role model, and as an advocate for gender equality in science".
*2019, Appointed to the University of Wollongong as Deputy Vice-Chancellor (Research and Innovation).
*2020, Leach Lecture and Medal, Lorne Protein Conference
*2023, Ralph Slatyer Medal and Lecture, Australian National University
Martin has held leadership roles on national and international committees. She is a former chair of the National Committee for Crystallography of the Australian Academy of Science (2008–2011), a past President of the Society for Crystallographers in Australia and New Zealand (2003–2005) and a former member of the Scientific Advisory Committee of the [http://www.synchrotron.org.au/ Australian Synchrotron] (2002–2009, 2015-18), the President of the [http://asca.iucr.org/ Asian Crystallography Association] (2016–2019) and a member of the Executive Committee of the [http://www.iucr.org/ International Union of Crystallography] (2017–2023). She is currently a Trustee of the Cambridge Crystallographic Data Centre (2023-) and Chair of the worldwide Protein Data Bank Advisory Committee (2022-).