The resistivity structure of Fogo volcano and the seismically active Congro region of São Miguel Island has been determined by 3-D inversion from 44 magnetotelluric soundings to yield new insights into the internal architecture of this volcanic island. Following comprehensive testing of processing codes to yield optimum magnetotelluric responses from the collected time-series, a robust electrical resistivity model was obtained. Sensitivity analysis of various features from the inversion process was used to determine their reliability, and aid geological interpretation. The magnetotelluric data imaged, and provided new structural insights into the Ribeira Grande geothermal system on the northern flank of Fogo volcano, where a shallow low resistivity (1 - 5Ωm) region has strong correlation with borehole data, and is shown to be an excellent proxy for mapping temperature and clay alteration mineralogy. Beneath the central edifice of Fogo volcano and also throughout the Congro region, the geology is very resistive, however the new magnetotelluric observations do not yield any further constraints on the origin of the seismicity that poses threats to the local populations residing on this hazardous island.