The origin of the nearly circular Colônia structure, located at the southwestern edge of the city of São Paulo, Brazil, has been the subject of a long‐standing debate, ever since the 1960s when the structure was first investigated by geophysical methods. The structure still raises interest for geological research, as its sedimentary infill holds important paleoclimatic information about the evolution of the tropical rainforest, as well as the interplay between the South American summer monsoon, the Intertropical Convergence Zone, and the southern Westerly wind belt—for possibly as long as several million years. In addition, the search for evidence to conclusively establish the origin of this structure continues, and the answer most likely lies in the lower portions of the basin's sedimentary infill, which also holds a significant potential for underground water resources. Here, we present the results from recent seismic (reflection and HVSR), gravimetric, and geoelectrical surveys. They have provided a reliable image of the sedimentary infill, and the maximum depth to basement within the structure has been constrained consistently by the different methods to approximately −400 m. The geophysical data have also allowed to map the lateral contact between the crystalline basement rocks and the sedimentary infill, which indicates a diameter of approximately 2.8 km for the sedimentary basin, with 3.6 km being the diameter of the outermost limit of the structure. A total of six seismic stratigraphic boundaries were identified within the sedimentary infill, providing a framework for the planning of a deep drilling campaign and subsequent sampling program aimed at geological and paleoclimatology studies.