Faulds worked as a postdoctoral researcher for  on the detection of DNA using surface-enhanced resonant Raman spectroscopy (SERRS). She became increasingly interested in the use of analytical chemistry to improve people's lives. Faulds was appointed as a lecturer in 2006.
Faulds was promoted to Reader in 2012 and Professor in 2015. Faulds works on the development of surface-enhanced Raman spectroscopy (SERS) for analytical detection. SERSs permits multiplexed and sensitive biological analysis. Her work uses signal amplification methods for the quantitative analysis of biomolecules, as the sensitivity allows her to detect target DNA and proteins. SERS also allows Faulds to make multiple measurements of different analytes in one sample. In 2015 she was the first woman and youngest person to ever be elected chair of the Infrared and Raman Discussion Group (IRDG). She has described C. V. Raman as her "hero of spectroscopy".
Her recent work has looked at the optical detection of Listeria using bionanosensors. The bionanosensors permit the multiplexed detection of pathogens, which can remove the risk of infectious diseases without the need for antimicrobial drugs. She covers SERS active magnetic nanoparticles with lectins, which can recognise and bind to carbohydrates in bacteria. These nanoparticles can collect and concentrate bacteria from production lines. Silver nanoparticles are functionalised with a biorecognition molecule, such as an aptamer, and Raman reporter, resulting in a SERS signal when a nanoparticle binds to the bacterial target. The magnetic component can then be studied further using portable Raman spectrometers.
Faulds is a founding member of Renishaw plc diagnostics, a University of Strathclyde spin-off company, and serves as its Director of Research. Faulds joined the editorial board of RSC Advances in November 2016 and as Associate Editor of Analyst in August 2020. She co-directs the Engineering and Physical Sciences Research Council (EPSRC) and Medical Research Council (MRC) Centre for Doctoral Training (CDT) in Optical Medical Imaging, shared between the University of Edinburgh and the University of Strathclyde.