As one kind of metal–organic framework material, zinc l-phenylalanine chelate may combine the merits of organic and inorganic components at the molecular level, thus making it a preferred anode active material. However, reports about zinc l-phenylalanine chelate anodes for lithium (Li) ion batteries are still scarce at the moment. Herein, shape-controlled synthesis of zinc l-phenylalanine chelate was carried out through a facile liquid-phase precipitation reaction and subsequent lyophilization. The obtained zinc l-phenylalanine chelate was investigated by field emission scanning electron microscopy, energy-dispersive X-ray spectroscopy, transmission electron microscopy, X-ray diffraction, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, thermogravimetric analysis, galvanostatic charge/discharge and cyclic voltammetry. The results suggest that zinc l-phenylalanine chelate appeared as uniform nanofibers about 140 nm diameter and 2–5 μm long. Furthermore, the zinc l-phenylalanine chelate nanofiber anode exhibited satisfactory electrochemical performances. For example, the initial specific discharge capacity was as high as 255 mAh/g at 100 mA/g and the reversible capacity remained 109 mAh/g even at 1000 mA/g for 200 cycles. Additionally, the possible lithium-storage mechanism was also explored. The synergistic effect of the combination of organic/inorganic components at the molecular level, regular nanofiber-like morphology and structural cavities may facilitate good strain accommodation, short ionic/electronic transport paths and high electrochemical performance.