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Two-dimensional metal carbides or nitrides (MXenes) demonstrate various excellent properties; however, their poor permeability precludes their application in water treatment. In this study, Ti3C2Tx MXene/nZVI/fungal hyphae nanofiber hybrid membranes (MXene/nZVI@FH) were prepared by chemical-intensive precipitation method for the robust capture of Be(II) from a beryllium-ammonia complexing solution. Interestingly, the MXene/nZVI@FH membrane showed favorable water permeability (6.10 × 10−15 m2), which was approximately 301 times higher than that of a pure Ti3C2Tx membrane, and 99.8% Be(II) was captured from the Be(NH2)2 complexing solution with an extremely low concentration (19.85 ppm). Specifically, the maximum Be(II) adsorption capacity of MXene/nZVI@FH was calculated to be 95.20 mg/g from the Be(NH2)2 complexing solution at pH 5.0 and 35 °C. Various characterization results (e.g., SEM, FTIR, XRD, VSM and XPS) suggested that Be(II) prefers to coordinate with surface oxygen groups bonded to the MXene nanosheets by forming BeO and BeO22− bidentate inner-sphere complexes. Furthermore, due to its reticular sandwiched structure, MXene/nZVI@FH could be easily activated and reused by leaching with 0.1 M HCl solution. Thus, it is a promising hybrid membrane for the removal and recovery of Be(II) from a Be(NH2)2 complexing solution.