The use of wastewater for CO₂ mineralization is a promising strategy that not only addresses environmental issues (i.e., preventing greenhouse gas emissions and algal blooms by CO₂ removal), but also produces economic benefits (i.e., recovery of carbonate-based minerals). In this study, we propose an innovative flow-electrode capacitive deionization (FCDI) system for efficient bicarbonate ion (HCO₃⁻) removal and ammonium bicarbonate (NH₄HCO₃) enrichment from synthetic swine wastewater, which commonly contains excessive ammonium ions (NH₄⁺) and HCO₃⁻. The effects of different operational parameters for HCO₃⁻ removal and enrichment were investigated. At optimal operating conditions, we achieved approximately 1.61 M of NH₄HCO₃ concentrated solution with 97.2% of purity in 30 h with a C removal rate of 1.01 kg C m⁻² d⁻¹ and energy consumption of 2.87 kWh kg⁻¹C. This is a removal rate of approximately 2–5 times greater than other electrochemical systems and 25% less energy consumption. In addition, the feasibility of the NH₄HCO₃ enrichment via the FCDI system was also verified by X-ray diffraction (XRD) analysis and Raman spectroscopy. This work provides an efficient strategy for NH₄HCO₃ enrichment from swine wastewater and a great potential to expand the scope of CO₂ utilization.