Pre‐clinical models are essential research tools before novel therapeutic or diagnostic methods can be applied to humans. These range from in vitro cell monocultures to vastly more complex animal models, but clinical translation to humans often fails to deliver significant results. Three‐dimensional organoid systems are being increasingly studied to establish physiologically relevant in vitro platforms in a trade‐off between the complexity of the research question and the complexity of practical experimental setups. The sensitivity and precision of analytical tools are yet another limiting factor in what can be investigated, and mass spectrometry is one of the most powerful analytical techniques available to the scientific community. Its innovative use to spatially resolve biological samples has opened many research avenues in the field of mass spectrometry imaging (MSI). Here, we aim to explore the current scientific landscape in the application of MSI on organoids, with an emphasis on their combined potential to facilitate and improve pre‐clinical studies.This article is protected by copyright. All rights reserved