The sedimentary basins of Loja, Malacatos-Vilcabamba and Catamayo belong to the Neogene-Quaternary synorogenic intramontane basins of South Ecuador. They were formed during uplift of the Andes since Middle-Late Miocene as a result of the Nazca plate subduction beneath the South American continental margin. This E-W compressional tectonic event allowed for the development of NNE-SSW oriented folds and faults, determining the pattern and thickness of sedimentary infill. New gravity measurements in the sedimentary basins indicate negative Bouguer anomalies reaching up to −292 mGal related to thick continental crust and sedimentary infill. 2D gravity models along profiles orthogonal to N-S elongated basins determine their deep structure. Loja Basin is asymmetrical, with a thickness of sedimentary infill reaching more than 1200 m in the eastern part, which coincides with a zone of most intense compressive deformation. The tectonic structures include N-S, NW-SE and NE-SW oriented folds and associated east-facing reverse faults. The presence of liquefaction structures strongly suggests the occurrence of large earthquakes just after the sedimentation. The basin of Malacatos-Vilcabamba has some folds with N-S orientation. However, both Catamayo and Malacatos-Vilcabamba basins are essentially dominated by N-S to NW-SE normal faults, producing a strong asymmetry in the Catamayo Basin area. The initial stages of compression developed folds, reverse faults and the relief uplift determining the high altitude of the Loja Basin. As a consequence of the crustal thickening and in association with the dismantling of the top of the Andes Cordillera, extensional events favored the development of normal faults that mainly affect the basins of Catamayo and Malacatos-Vilcabamba. Gravity research helps to constrain the geometry of the Neogene-Quaternary sedimentary infill, shedding some light on its relationship with tectonic events and geodynamic processes during intramontane basin development.