This study combined geophysical, geologic, and topographic information to investigate the Mayarí-Baracoa ophiolitic belt in eastern Cuba. A recently developed interpretation technique for 3D inversion of magnetic data was employed to determine the geometry at depth of ophiolitic and other rocks. Based on measured susceptibilities, lithologies were divided into four groups. The geophysical data allowed 3D imaging of ophiolites (serpentinized peridotites and gabbros), as well as sedimentary and volcanic rocks. The study verified that both the Pinares de Mayari Plateau and the Sagua de Tánamo Basin have been strongly influenced by tectonic activity. The modeling showed evidence of more east-west structural deformation of the ophiolite belt than had been previously reported. The depth of the depocenter of the Sagua de Tánamo basin and its rate of subsidence were determined. We identified some areas with potential for economic deposits of chromium, cobalt, and nickel, as well as precious metals; these were related to the thickness of the peridotite layer. The modeling also corroborated the presence of previously mapped faults and revealed other previously unrecognized faults.