Dr Khanna started her career as an Agricultural Research Scientist with the Indian Council for Agricultural Research in 1991 and joined the National Research Centre on Plant Biotechnology, New Delhi in 1992. She developed transformation technologies for improvement of indica rice as part of Rockefeller Foundation´s rice biotechnology program and generated one of India´s first insect resistant Bt basmati rice lines. In 2000, she moved to University of Southern Queensland, Toowoomba and worked on a GRDC funded project to generate frost resistant transgenic wheat lines. In 2002, she joined Prof James Dale at QUT, Brisbane to develop Agrobacterium–mediated transformation system for banana. After successfully completing that project, she continued with Prof Dale´s group on a CRC SIIB funded project aimed at developing sugarcane as a biofactory using a controlled and inducible system (InPACT: In–plant activation of transgene) for activating transgenes (2004–2006).
Since 2006 she is working as the senior scientist at QUT on the Grand Challenges for Global Health Project funded by the Bill and Melinda Gates Foundation. The project involves genetic engineering of bananas for nutritional biofortification. In this role she is leading the laboratory team at QUT and is also actively involved in technology transfer to the collaborating partner team at National Agricultural Research Organisation, Uganda. She also led a project on development of efficient transformation systems for Australian sugarcane cultivars and is currently also involved in developing drought–tolerant sugarcane using anti–apoptosis genes. In addition, she is also involved in research on use of R genes and anti–apoptosis genes for generating fungal–resistant bananas.