This article presents a thermomechanical triaxial cell modified to fit inside a synchrotron X-ray diffraction (XRD) beamline aiming to assess thermally induced microstructural changes in saturated clays under in situ conditions. Understanding these thermally induced microstructural alternations in clays will explain some of the poorly understood or misunderstood concepts about the thermomechanical behavior of these soils; this, in turn, will allow more robust designs of geostructures for thermal and energy applications. Compared to other techniques, synchrotron diffraction provides (1) high accuracy and sensitivity to small changes compared to benchtop XRD and (2) the ability to assess microstructure changes under in situ conditions (i.e., stress, saturation, and temperature). The design and selection of the various materials used in the modified triaxial cell are first presented. Based on this design, it is recommended to use (1) sample diameters in the 5 to 7–mm range to minimize sample disturbance during trimming and X-ray background scattering during X-ray scans and (2) a transparent cell with acrylic walls, with nitrogen gas as the confining fluid and neoprene membranes, since all considered cell wall materials (i.e., acrylic and aluminum), confining gases (i.e., nitrogen, carbon dioxide, argon, and compressed air), and membrane materials (i.e., latex and neoprene) result in accurate diffraction measurements. The modified cell was then used to assess the changes in particle reorientations of a normally consolidated kaolinite clay after the saturation and consolidation stages as well as the heating load. The results showed that the saturation and consolidation stages reoriented the particles perpendicular to the longitudinal axis of the sample, which is the same direction as the pore water flowing in and out of the sample. Further particle reorientations were observed due to heating.