Encapsulation of ionic liquids (ILs) has been shown to be an effective technique to overcome slow mass transfer rates and handling difficulties that stem from the high viscosity of bulk ILs. These systems commonly rely on diffusion of small molecules through the encapsulating material (shell), into the IL core, and thus the composition of the shell impacts uptake performance. Herein, we report the impact of polymer shell composition on the uptake of the small molecule dye methyl red from water by encapsulated IL. Capsules with core of 1-hexyl-3-methylimidazolium bis(trifluorosulfonyl)imide ([Hmim][TFSI]) were prepared by interfacial polymerization in emulsions stabilized by graphene oxide (GO) nanosheets; the use of different diamines and diisocyanates gave capsule shells with polyureas that were all aliphatic, aliphatic/aromatic, and aliphatic/polar aprotic. These capsules were then added to aqueous solutions of methyl red at different pH values, and migration of the dye into the capsules was monitored by UV-vis spectroscopy, compared to the capsule shell alone. Regardless of the polymer identity, similar extents of dye uptake were observed (>90% at pH = 2), yet capsules with shells containing polyureas with polar aprotic linkages took longer to reach completion. These studies indicate that small changes in capsule shell composition can lead to different performance in small molecule uptake, giving insight into how to tailor shell composition for specific applications, such as solvent remediation and gas uptake.