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Three hydrophobic ionic liquids (ILs) based on the bis(trifluoromethylsulfonyl)imide anion were studied in terms of the relative hydrophobicity of the equilibrium phases. The ILs were 1-methyl-1-propylpiperidinium bis(trifluoromethylsulfonyl)imide, [C3mpip][NTf2]; 1-methyl-1-propylpyrrolidinium bis(trifluoromethylsulfonyl)imide, [C3mpyrr][NTf2]; and 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide, [C4mpyrr][NTf2]. In addition, the liquid–liquid phase diagrams were determined for two of the ILs, namely, [C3mpip][NTf2] and [C3mpyrr][NTf2]. The compositions of the equilibrium phases were obtained using a gravimetric technique in the temperature range from 278.15 to 343.15 K. The immiscibility gaps for these systems were found to be very large, with that for the system [C3mpip][NTf2] + water being slightly wider than that for the system [C3mpyrr][NTf2] + water. Partition coefficients for a series of dinitrophenylated (DNP) amino acids in the three systems at 296.15 K were experimentally determined. The DNP amino acids were found to distribute preferentially to the water-rich phase, and the partition was more extreme for the system with [C3mpip][NTf2]. The experimental partition coefficients decreased as the size of the alkyl side chain in the solutes increased. The relative hydrophobicity of the equilibrium phases was assessed by means of the free energy of transfer of a methylene group between the phases, ΔG(CH2), calculated from the partition coefficients of the series of solutes. It was found that the relative hydrophobicity between the phases follows the order [C4mpyrr][NTf2] > [C3mpip][NTf2] > [C3mpyrr][NTf2].