Describing and understanding surface chemistry on the atomic scale is of primary importance in predicting and rationalize nanoparticle morphology as well as their physical and chemical properties. Here we present the results of comprehensive density functional theory studies on the adsorption of several small organic species, representing the major species (H2, Cl2, HCl, NH3, NH4Cl, and CH3COOH), present in the reaction medium during colloidal iron nanoparticle synthesis on various low-index iron surface models, namely, (100), (110), (111), (211), and (310). All of the tested ligands strongly interact with the proposed surfaces. Surface energies are calculated and ligand effects on the morphologies are presented, including temperature effects, based on a thermodynamic approach combined with the Wulff construction scheme. The importance of taking into account vibrational contributions during the calculation of surface energies after adsorption is clearly demonstrated. More importantly, we find that thermodynamic ligand effects can be ruled out as the unique driving force in the formation of recently experimentally observed iron cubic nanoparticles.