There is growing interest in flexible, cost-effective, and binder-free energy storage devices to meet the special needs of modern electronic systems. Herein we report a general, scalable, eco-friendly, and cost-effective approach for the fabrication of nano-Fe3O4-anchored three-dimensional (3D) carbon nanofiber (CNFs) aerogels (Fe3O4@BC-CNFs). The preparation processes include the anchoring of Fe2O3 nanoparticles on bacterial cellulose (BC) nanofibers with intrinsic 3D network structure and subsequent carbonization at different temperatures. The aerogel carbonized at 600 °C (Fe3O4@BC-CNFs-600) is highly flexible and was directly used as working electrodes in lithium-ion batteries without metal current collectors, conducting additives, or binders. The Fe3O4@BC-CNFs-600 demonstrates greatly improved electrochemical performance in comparison to the bare Fe3O4 nanoparticles. In addition to its excellent flexibility, a stable capacity of 755 mAh g−1 for up to 80 cycles is also higher than most of carbon-Fe3O4 hybrids. The high reversible capacity and excellent rate capability are attributed to its 3D porous network structure with well-dispersed Fe3O4 nanoparticles on the surfaces of CNFs.