Ion concentration polarization (ICP) accomplishes preconcentration for bioanalysis by localized depletion of electrolyte ions, thereby generating a gradient in electric field strength that facilitates electrokinetic focusing of charged analytes by their electromigration against opposing fluid flow. Such ICP focusing has been shown to accomplish up to a million-fold enrichment of nucleic acids and proteins in single-stage preconcentrators. However, the rate at which the sample volume is swept is limited, requiring several hours to achieve these high enrichment factors. This limitation is caused by two factors. First, an ion depleted zone (IDZ) formed at a planar membrane or electrode may not extend across the full channel cross section under the flow rate employed for focusing, thereby allowing the analyte to “leak” past the IDZ. Second, within the IDZ, large fluid vortices lead to mixing, which decreases the efficiency of analyte enrichment and worsens with increased channel dimensions. Here, we address these challenges with faradaic ICP (fICP) at a three-dimensional (3D) electrode comprising metallic microbeads. This 3D-electrode distributes the IDZ, and therefore, the electric field gradient utilized for counter-flow focusing across the full height of the fluidic channel, and its large area, microstructured surface supports smaller vortices. An additional bed of insulating microbeads restricts flow patterns and supplies a large area for surface conduction of ions through the IDZ. Finally, the resistance of this secondary bed enhances focusing by locally strengthening sequestering forces. This easy-to-build platform lays a foundation for the integration of enrichment with user-defined packed bed and electrode materials.