This article presents a method for producing chiral ionic liquid-based polyurea microcapsules that can be magnetically separated. The method involves entrapping hydrophilic magnetic nanoparticles within chiral polyurea microspheres. The synthetic process for creating these magnetic polyurea particles involves oil-in-oil (o/o) nano-emulsification of an ionic liquid-modified magnetite nanoparticle (MNPs-IL) and an ionic liquid-based diamine monomer, which comprises a chiral bis(mandelato)borate anion, in a nonpolar organic solvent, toluene, and contains a suitable surfactant. This is followed by an interfacial polycondensation reaction between the isocyanate monomer, polymethylenepolyphenyl isocyanate (PAPI 27), and the chiral diamine monomer, which generates chiral polyurea microcapsules containing magnetic nanoparticles within their cores. The microcapsules generated from the process are then utilized to selectively adsorb either the R or S enantiomer of tryptophan (Trp) from a racemic mixture that is dissolved in water, in order to evaluate their chiral recognition capabilities. During the experiments, the magnetically separable chiral poly(ionic liquid) microcapsules, which incorporated either the R or S isomer of chiral bis(mandelato)borate, exhibited exceptional enantioselective adsorption performance. Thus, the chiral polymeric microcapsules embedded with the R-isomer of the bis(mandelato)borate anion demonstrated significant selectivity for adsorbing L-Trp, yielding a mixture with 70% enantiomeric excess after 96 h. In contrast, microcapsules containing the S-isomer of the bis(mandelato)borate anion preferentially adsorbed D-Trp, achieving an enantiomeric excess of 73% after 48 h.