The characterization of separators for Li-ion or Li-metal batteries incorporating hydrophobic ionic liquid electrolytes is reported herein. Ionic liquids made of N-butyl-N-methylpyrrolidinium (PYR14+) or N-methoxyethyl-N-methylpyrrolidinium (PYR12O1+), paired with bis(trifluoromethanesulfonyl)imide (TFSI-) or bis(fluorosulfonyl)imide (FSI-) anions, were tested in combination with separators having different chemistries and morphologies in terms of wetting behavior, Gurley and McMullin number, as well as Li/(Separator+Electrolyte) interfacial properties. It is shown that non-functionalized microporous polyolefin separators are poorly wetted by FSI--based electrolytes (contrary to TFSI--based electrolytes), while the ceramic coated separator Separion® allows good wetting with all electrolytes. Furthermore, by comparing the lithium solid electrolyte interphase (SEI) resistance evolution at open circuit and during cycling, depending on separator morphologies and chemistries, it is possible to propose a scale for SEI forming properties in the order: PYR12O1FSI>PYR14FSI>PYR14TFSI>PYR12O1TFSI. Finally, the impact the separator morphology is evidenced by the SEI resistance evolution and by comparing Li electrodes cycled using separators with two different morphologies.