The fabrication of Ru nanostructures by focused electron beam induced deposition (FEBID) requires suitable precursor molecules and processes to obtain the pure metal. So far this is problematic because established organometallic Ru precursors contain large organic ligands, such as cyclopentadienyl anions, that tend to become embedded in the deposit during the FEBID process. Recently, (η3-C3H5)Ru(CO)3X (X = Cl, Br) has been proposed as an alternative precursor because CO can easily desorb under electron exposure. However, allyl and Cl ligands remain behind after electron irradiation and the removal of the halide requires extensive electron exposures. Auger electron spectroscopy is applied to demonstrate a postdeposition purification process in which NH3 is used as a reactant that enhances the removal of Cl from deposits formed by electron irradiation of thin condensed layers of (η3-C3H5)Ru(CO)3Cl. The loss of CO from the precursor during electron-induced decomposition enables a reaction between NH3 and the Cl ligands that produces HCl. The combined use of electron-stimulated desorption experiments and thermal desorption spectrometry further reveals that thermal reactions contribute to the loss of CO in the FEBID process but remove only minor amounts of the allyl and Cl ligands.