The conductive and capacitive material properties of the subsurface can be quantified through the frequency-dependent complex resistivity. However, the routine three-dimensional (3D) interpretation of voluminous induced polarization (IP) data sets still poses a challenge due to large computational demands and solution nonuniqueness. We have developed a flexible methodology for 3D (spectral) IP data inversion. Our inversion algorithm is adapted from a frequency-domain electromagnetic (EM) inversion method primarily developed for large-scale hydrocarbon and geothermal energy exploration purposes. The method has proven to be efficient by implementing the nonlinear conjugate gradient method with hierarchical parallelism and by using an optimal finite-difference forward modeling mesh design scheme. The method allows for a large range of survey scales, providing a tool for both exploration and environmental applications. We experimented with an image focusing technique to improve the poor depth resolution of surface data sets with small survey spreads. The algorithm's underlying forward modeling operator properly accounts for EM coupling effects; thus, traditionally used EM coupling correction procedures are not needed. The methodology was applied to both synthetic and field data. We tested the benefit of directly inverting EM coupling contaminated data using a synthetic large-scale exploration data set. Afterward, we further tested the monitoring capability of our method by inverting time-lapse data from an environmental remediation experiment near Rifle, Colorado. Similar trends observed in both our solution and another 2D inversion were in accordance with previous findings about the IP effects due to subsurface microbial activity.