The synchrotron through-the-substrate X-ray microdiffraction technique (tts-μXRD) is extended to the structural study of microvolumes of crystals embedded in polished thin sections of compact materials [Rius, Labrador, Crespi, Frontera, Vallcorba & Melgarejo (2011). J.Synchrotron Rad.18, 891–898]. The resulting tts-μXRD procedure includes some basic steps: (i) collection of a limited number of consecutive two-dimensional patterns (frames) for each randomly oriented crystal microvolume; (ii) refinement of the metric from the one-dimensional diffraction pattern which results from circularly averaging the sum of collected frames; (iii) determination of the reciprocal lattice orientation of each randomly oriented crystal microvolume which allows assigning the hkl indices to the spots and, consequently, merging the intensities of the different frames into a single-crystal data set (frame merging); and (iv) merging of the individual crystal data sets (multicrystal merging) to produce an extended data set suitable for structure refinement/solution. Its viability for crystal structure solution by Patterson functiondirect methods (δ recycling) and for accurate single-crystal least-squares refinements is demonstrated with some representative examples from petrology in which different glass substrate thicknesses have been employed. The section of the crystal microvolume must be at least of the same order of magnitude as the focus of the beam (15 × 15 µm in the provided examples). Thanks to its versatility and experimental simplicity, this methodology should be useful for disciplines as disparate as petrology, materials science and cultural heritage.