Three distinct Ge nanoparticle-filled carbon nanofiber (CNF) composites, Ge@CNF, Ge@C@CNF and Ge@CNF@C, were fabricated by chemical vapor deposition (CVD) and electrospinning techniques. These different structures were prepared by: 1) dispersing Ge nanoparticles into CNF, 2) adding carbon-coated Ge nanoparticles (Ge@C) prepared by CVD into CNF, and 3) depositing CVD carbon onto Ge@CNF, respectively. Compared with the Ge@CNF composite, both Ge@C@CNF and Ge@CNF@C had additional amorphous carbon coating fabricated by the CVD method. The three composites were studied as binder-free electrodes for rechargeable lithium-ion batteries. Raw Ge anode materials suffered from serious volume changes and nanoparticle aggregations during cycling, resulting in pulverization and capacity loss. However, carbon nanofiber and the supplemental CVD carbon layer in these nanofiber composites could help preserve the structural integrity of the alloy anode materials during repeated cycling, and consequently, lead to improved cycling stability. In this work, it was found that among the three composites, Ge@CNF@C exhibited the highest capacity retention of 89% at the 50th cycle due to the structurally-durable thorn-like Ge morphology and the additional CVD carbon confinement. Ge@CNF and Ge@C@CNF encountered rapid capacity loss because large Ge clusters were formed and jeopardized the integrity of the electrode structure during cycling.