In the development of analytical methodologies to perform chiral separations, capillary electrophoresis (CE) is a well-established and one of the most powerful separation techniques. Although cyclodextrins (CDs) are by far the most employed chiral selectors to achieve the enantiomeric separation of a broad variety of chiral compounds of relevance in different scientific fields, in some cases, the desired enantiomeric separation is not possible using only CDs. Thus, the use of advanced materials has attracted considerable attention to develop novel chiral systems in which these materials can be used in single systems or combined with other chiral selectors. In this context, chiral ionic liquids (CILs) have emerged as promising materials for tuning the selectivity in chiral analysis. An interesting group of CILs is the amino acid-based ionic liquids (AAILs). To illustrate the great possibilities of these AAILs in the field of chiral separations, this chapter describes the main experimental points to be taken into consideration in the application of two different CE approaches based on the combined use of chiral AAILs and CDs. The first example describes the use of hydroxypropyl-β-CD in combination with tetrabutylammonium-l-lysine for the enantiomeric determination of econazole or sulconazole in pharmaceutical formulations by electrokinetic chromatography (EKC). The second example illustrates the application of an EKC methodology based on the combined use of γ-cyclodextrin and l-carnitine-based ionic liquid for the enantiomeric separation of cysteine in dietary supplements.