Frequency-domain electromagnetic induction (FD-EMI) sensors using a double magnetic dipole (loop–loop) geometry are efficient tools to rapidly sense the electrical and magnetic properties of the subsurface. Recent progress, including the development of multiconfiguration FD-EMI systems, efficient acquisition strategies using total-station tracked platforms, and fast full 3-D inversion procedures, allows the reconstruction of 3-D subsurface electrical and magnetic properties distributions with unprecedented details. In this study, we analyze the capabilities of a recently proposed multichannel deconvolution (MCD) procedure for the 3-D inversion of low $S/N$ FD-EMI inphase data. By using a synthetic experiment, we demonstrate how such a method can unveil subsurface magnetic signatures, which might be hardly detected by a qualitative analysis of the data space without inversion. We further confirm these observations using a field dataset acquired at a Gallo-Roman archeological site in Orcines, France. Here, the 3-D MCD of FD-EMI inphase data unveils the presence of archeological remains that are not visible in the original inphase data maps. In addition, the overall appearance of the image is improved with better-resolved signatures. This study confirms the limitations of qualitative analysis of FD-EMI data and thereby demonstrates the potential of 3-D acquisition and interpretation procedures, which are able to optimally exploit the information provided by FD-EMI inphase data.