Halloysite nanotubes (often abbreviated as HNTs) are technologically important owing to their unique structural and morphological features. Some of these features pre-exist in the naturally hydrated halloysite-(10 Å) parent clay mineral; others may develop during its dehydration towards halloysite-(7 Å). This is the first infrared spectroscopic study of the transition to halloysite-(7 Å), which, in combination with X-ray diffraction (XRD), aimed at advancing the structural description of the process. Three cylindrical and two polygonal halloysite-(10 Å) samples, in both their H- and D-forms, were measured by attenuated total reflectance (ATR), non-invasively and in situ, following step-wise equilibration from 70% relative humidity (RH) to <10% RH and back to 70% RH at ambient temperature. This approach allowed for recording the spectrum of the dehydrating (but not rehydrating) interlayer in the νO–D range, without interference from the inner νOH groups, or from the inner-surface νOH of anhydrous interlayers already present in the parent material. Besides the well-known ‘hole’ H2O species, a new type of H2O-decorated defect was detected at frequencies normally dominated by the inner νOH. This defect is linked to the microenvironment created by the detachment between layer packets and forming ‘crevices’ or ‘slits’ upon dehydration. In addition, the study of the νSi–O spectrum demonstrated that the dehydration of halloysite-(10 Å) leads to the parallel formation of localized, ordered, kaolinite-like domains co-existing with regions of accumulated disorder. The as-produced halloysite-(7 Å) had a non-ideal, open structure that resisted rehydration because the kaolinite-like domains do not rehydrate and act as permanent cross-links.