The Soultz-sous-Forets site (Alsace, France) is the first pilot geothermal project in the world that furnished the proof of concept of enhanced geothermal systems by producing energy from a deep-seated granite. The Alsace region, with its hundreds of previous drillings and seismic history related to both oil and potash exploitation, has been shown to have high subterranean temperatures. In the Soultz-sous-Forets geothermal project, most attention has focused on the basement and the sedimentary cover/basement interface. Thus, the sedimentary portion of the well (approximately 1.4 km thick) has never been fully investigated. The only available data on the Soultz-sous-Forets sedimentary cover are from an old masterlog (GPK-1) with interpretations of the tops and bases of the main geological formations, and from some other less well-documented well logs (EPS-1 and GPK-2). The main challenge of this work is therefore to re-interpret the old well data to provide precise and detailed chrono-lithostratigraphic logs for GPK-1 and GPK-2, especially in their sedimentary portions. These new investigations of the GPK wells have been possible due to the new data collected in the recent geothermal wells at Rittershoffen (GRT-1 and GRT-2, located 6.5 km from Soultz-sous-Forets), which are characterized by a quite complete stratigraphic succession. Both sites have been explored by deep drilling operations aiming to exploit the heat extracted from a deep granitic basement (Palaeozoic) covered by a stack of 1.4- and 2.2-km-thick sedimentary rocks (Mesozoic to Cenozoic) at Soultz-sous-Forets and Rittershoffen, respectively. Thus, the Rittershoffen chrono-lithostratigraphic logs have been used as a baseline to interpret the sedimentary succession in GPK-1 and GPK-2. In conclusion, all the well logs are compared for stratigraphic comparisons. With approximately 1400 m of sedimentary cover at Soultz-sous-Forets instead of 2200 m at Rittershoffen, the correlation between the two sites showed many differences exist in the sedimentary columns: layers missing due to erosion, lateral thickness variations in formations, and—above all—the occurrence of at least four major fracture zones affecting the units. In addition, a structural analysis was made to more precisely define the limits of the geological formations observed and to present more arguments for the presence of fracture zones or faults.