The success of time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging is dependent on effective sputtering and ionisation of analytes from the sample surface imaged. Although there have been significant advances in SIMS analysis, thanks to the advent of cluster ion beams, this has largely been in the sputtering process. Ionisation is still largely ineffective, and improvements in this direction would significantly enhance SIMS imaging. We are specifically interested in improving the capabilities of SIMS imaging for detecting metabolites (small molecular weight components of metabolism) in biological cells and tissues. Here, we report a method to enhance the signal intensities of diagnostic ions and improve SIMS imaging of metabolites using a vapour-mediated ion activation approach. Exposure of a synthetic cocktail of metabolites to ammonia vapour showed a greater than threefold increase in the deprotonated ion signals for some of the metabolites in the cocktail. However, room temperature exposure resulted in changes to the sample morphology, indicating that the sample surface was disrupted. It was possible to increase the ion yield and retain the sample morphology when the treatment was carried out at 4 °C. Application of the methodology to a plant tissue section showed the detection of signals that were not observed in the samples that were not treated. This is a promising approach that can be applied to enhance the detection of diagnostic ions for the ToF-SIMS analysis of organic and biological samples. Copyright © 2012 John Wiley & Sons, Ltd.