The stereoselective formation of 1,2-cis glycosidic linkages is challenging. The currently most widely used strategy for their installation uses 4,6-O-benzylidene protected building blocks. The stereoselectivity of this reaction is thought to be driven by a covalent intermediate, which reacts via an SN2 mechanism. However, the role of cationic SN1-type intermediates in this reaction is unclear. Here, we elucidate the structure of glycosyl cations carrying 4,6-O-benzylidene groups using cryogenic infrared ion spectroscopy and computational methods. The data reveal that the intermediates unexpectedly form anhydro cations, which correlates well with the stereoselective outcome of SN1-type glycosylations. The study highlights how cryogenic infrared spectroscopy can unravel novel intermediates in sugar chemistry and how this structural data can be linked to reactions in solution.