Ionic liquids (ILs) including oxalatoborate anions, like bis(oxalato)borate (BOB) and difluoro(oxalato)borate (DFOB) are extensively used in the battery sector as additives to promote the formation of protective layers on the surface of high-voltage cathode materials. In this work four ILs have been synthesized: N-ethoxyethyl-N-methylpiperidinium bis(oxalato)borate (PIP1,2O2BOB), N-ethoxyethyl-N-methylpiperidinium difluoro(oxalato)borate (PIP1,2O2DFOB), N-propyl-N-methylpiperidinium bis(oxalato)borate (PIP1,3BOB) and N-propyl-N-methylpiperidinium difluoro(oxalato)borate (PIP1,3DFOB) and their thermal properties have been linked to their structure. The presence of an oxygen atom in the PIP1,2O2 lateral chain suppresses crystallization of the ILs. Furthermore, PIP1,2O2DFOB shows a lower glass transition temperature than PIP1,2O2BOB. These observations have been explained using a combined molecular dynamics and density functional theory approach and an increase in the degree of freedom of the lateral chain of the cation due to the ether oxygen has been found. Comparing PIP1,2O2DFOB and PIP1,2O2BOB, a notable interaction between different domains of the anions is observed and is stronger in the DFOB case due to the charge-delocalization induced by the fluorine atoms, which generates a relatively positive charge on the boron atom. This is correlated to the weaker cation-anion attraction which hinders the glass transition of PIP1,2O2DFOB.