In this work, palladium nanoparticles (PdNps) were synthesized by reducing palladium chloride with sodium borohydride (NaBH4) aqueous solutions in presence of organic capping ligands such as β-cyclodextrin (βCD), an amphiphilic imidazole-based Ionic Liquid (C12mimBr) and an amphiphilic βCD derivative (βCDMOD14). The results demonstrated that the molecular organization of the capping agents has an important role in the stability of colloidal solution of PdNPs. In particular, the stability of PdNPs coated with βCDMOD14 ([email protected]βCDMOD14) can be controlled by changing the pH of the colloidal suspension. In addition, we propose that during the synthesis of PdNps and capped with C12mimBr ([email protected]12mimBr), the source of palladium is a coordination complex formed due to the presence of C12mimBr. Additionally, we studied the catalytic activity of [email protected]βCDMOD14 and [email protected]12mimBr using the reduction reaction of aromatic nitro compounds to aromatic amine in the presence of NaBH4, as a model in the remediation of aqueous phase. The kinetic data were modeled to the Langmuir–Hinshelwood equation that allows us to discriminate the affinity of 4-NP and NaBH4 towards modified surface of NPs in terms of their association constants (K4-NP, KBH4).