Proteins are long linear molecular chains that when folded into complex three‐dimensional shapes enable them to perform their biological functions. Infrared spectroscopy is a powerful technique for characterising protein folds, especially the proportions of helices and sheets that are significant building blocks in the overall structure. Traditionally, it was only possible to record infrared spectra from large amounts of material. In this paper, we show that it is possible to record the equivalent of the infrared spectrum from regions much smaller than a cell using a high‐performance spectrometer coupled to electron microscopy. One great advantage is that the spectroscopic measurements can be combined with the standard high‐resolution imaging and other characterisation techniques available in the electron microscope. We believe expansion of this method will impact diseases such as Alzheimer's, which are believed to be the results of an incorrect folding process. Our technique, where we combine infrared spectroscopic measurements with electron microscopy, could be invaluable in characterising the critical early stages of protein misfolding and/or assembly. This information will be invaluable in disease prognosis and the search for potential therapies.