The Campi Flegrei caldera experienced an unrest phase dating to 2005, which primary expression is the impressive ground uplift, accompanied by increasing degassing and seismic activities. Such last two phenomena developed mainly in the caldera central sector, including the Solfatara–Pisciarelli complex. However, the inner structure of such an area is still not defined, and this originates a poor understanding of the ongoing unrest. This paper describes the results of a new magnetotelluric survey performed in the Campi Flegrei caldera central sector. Through the inversion of data collected in 47 independent soundings, a 3D model of the electrical resistivity has been retrieved, which evidenced a partition of the investigated structure. The Agnano–Astroni area seems to be associated with a liquid-dominated geothermal reservoir, whereas the Solfatara–Pisciarelli area seems to be characterized by a single mixed liquid and gasses-dominated geothermal reservoir, which supplies the main caldera fumaroles. The proposed reconstruction of the geometrical characteristics of the hydrothermal system and the primary fluid rising pathways gives substantial clues about the significance of the detected structures in the evolution of the caldera unrest.