Controlled synthesis of anisotropic iron oxide nanoparticles is a challenge in the field of nanomaterial research that requires an extreme attention to detail. In particular, following up a previous work showcasing the synthesis of magnetite nanorods (NRs) using a two-step approach that made use of polyethylenenemine (PEI) as a capping ligand to synthesize intermediate β-FeOOH NRs, we studied the effect and influence of the capping ligand on the formation of β-FeOOH NRs. By comparing the results reported in the literature with those we obtained from syntheses performed (1) in the absence of PEI or (2) by using PEIs with different molecular weight, we showed how the choice of different PEIs determines the aspect ratio and the structural stability of the β-FeOOH NRs and how this affects the final products. For this purpose, a combination of XRD, HRTEM, and direct current superconducting quantum interference device (DC SQUID) magnetometry was used to identify the phases formed in the final products and study their morphostructural features and related magnetic behavior.