Prof. Aharoni is the recipient of the Andre Deloro price for outstanding research and significant breakthroughs in the fields of metabolomics, plant and environmental sciences, Weizmann Institute of Science, 2016.
The James Heineman Research Award for Biological and Biomedical research, 2010.
Prof. Aharoni is the recipient of the Weizmann Institute Scientific Council Prize (Levinson prize in Biology), 2008.
Prof. Aharoni is the recipient of the ERC (European Research Council) grant for Starting Independent Investigators, 2008.
Prof. Aharoni is the recipient of the Yigal Alon Fellowship award by the Council for Higher Education in Israel, 2005.
Prof. Aharoni is the recipient of the Sir Charles Clore Prize, 2004, Israel.