The study of nanocrystalline phase atomic ordering is intrinsically complicated. The presence of additional crystalline phase(s) exacerbates this challenge. Here, we use the synchrotron pair distribution function (PDF) to characterize the local atomic order of the nanocrystalline phases in ye’elimite-containing pastes. Here, a multi r-range analysis approach has been used, where the 30–50 Å r-range allows determining the crystalline phase contents and the 1.6-35 Å is used to characterize the atomic ordering in the nanocrystalline components. Quantitative phase contents have been also derived from these analyses. Specifically, we have prepared five stoichiometric ye’elimite pastes with variable anhydrite and water contents. For the pastes without anhydrite addition, ettringite was not present and two calcium aluminium monosulfate phases were required for good PDF fits. In addition to crystalline AFm (c =28.6 Å), a nanocrystalline AFm phase with a significantly smaller c-unit cell parameter value, c =26.8 Å, was required having about 60 Å of particle size. For a paste obtained with 31 wt% of anhydrite addition, the main crystalline phase was ettringite with the aluminium hydroxide having nano-gibbsite local structure with a quite small average particle size, =35 Å