Gouverneur won the AstraZeneca Research Award for organic chemistry in 2005.[8] She was the 2008 winner of the Royal Society of Chemistry (RSC) Bader Award, "for her important contributions to synthetic organofluorine chemistry."[12] In 2010, she was elected Fellow of the Royal Society of Chemistry[13] and received the IUPAC Distinguished Woman in Chemistry Award.[14] In 2011 she was awarded the Liebig Lectureship Award of the Organic Division of the German Chemical Society.[15] In 2012, she was holding the Blaise Pascal Chair (ENS/CEA, France).[16][17] In 2013, the UK's Royal Society selected her as one of 27 Royal Society Wolfson Research Merit Award holders.[18] In 2015, Gouverneur received the American Chemical Society Award for Creative Work in Fluorine Chemistry "for her contribution to late-stage fluorination and for invigorating creatively the field of [18F] radiochemistry for applications in Positron Emission Tomography."[19] In 2016, she was an International Visiting Research Scholar of the Peter Wall Institute for Advanced Studies (University of British Columbia)[20] and held the Tetrahedron Chair at the Belgian Organic Synthesis Symposium (BOSS) meeting.[21] That year, she received the RSC Tilden Prize for her interdisciplinary work in the area of organofluorine chemistry and radiochemistry, and the impact of her discoveries in medicine.[22][23]
In 2024 Gouverneur was awarded Royal Society The Davy Medal for contributions to the field of fluorine chemistry with applications in both medicine and positron emission tomography imaging.[32]