The crystal structure of sub-15 nm AMoO(4) (A = Ca, Sr, Bo) scheelite nanocrystals has been investigated using a dual-space approach that combines Rietveld and pair distribution function (PDF) analysis of synchrotron X-ray diffraction data. Rietveld analysis yields an average crystal structure in which the Mo-O bond distance exhibits an anomalously large contraction (2.8%) upon chemical substitution of Ba2+ for Ca2+. Such a dependence on chemical composition contradicts the well-known rigid character of Mo-VI-O bonds and the resulting rigidity of MoO4 tetrahedra in scheelites. Unlike Rietveld, PDF analysis yields a local crystal structure in which the Mo-O bond distance shows a negligible contraction (0.4%) upon going from Ba2+ to Ca2+ and, therefore, appears independent of the chemical composition. Analysis of the anisotropic displacement parameters of the oxygen atom reveals that the disagreement between the average and local structural models arises from the presence of static orientational disorder of the MoO4 tetrahedra. Rietveld analysis averages the random rotations of the MoO4 tetrahedra across the scheelite lattice yielding an apparent Mo-O bond distance that is shorter than the true bond distance. In contrast, PDF analysis demonstrates that the structural integrity of the MoO4 tetrahedra remains unchanged upon chemical substitution of the alkaline-earth cation, and that their orientational disorder is accommodated through geometric distortions of the AO(8) dodecahedra.