Analyte focusing by micelle to cyclodextrin stacking (MCDS) in micellar electrokinetic chromatography (MEKC) using sodium dodecyl sulfate (SDS) and fused silica capillaries is demonstrated for neutral, cationic, and chiral analytes. The stacking was at a dynamic boundary formed between the injected charged SDS micelles and neutral γ-cyclodextrin (γ-CD) zones, where the analytes bound inside micelles were released due to the formation of stable SDS-CD inclusion complexes. The complex formation reduced or eliminated the affinity of the analytes to the micellar phase. There was reversal (for charged) or nulling (for neutrals) of the analyte's effective electrophoretic mobility that caused the analytes to accumulate at the boundary. Under the conditions where the SDS micelles velocity is faster than the electroosmotic flow (using acidic buffer), MCDS was conducted by injection of a long plug of sample in a micellar diluent after injection of a CD solution plug into a capillary that was filled with MEKC background solution. By simply extending the length of the CD plug, chiral separations of chlorpheniramine and phenoxyacid herbicides were achieved without optimizing the MEKC conditions. The analytical figures of merit including linearity and repeatability for the tested compounds were found acceptable, and the sensitivity enhancement factors were up to 171. The stacking strategy in MEKC was applied to metabolic stability studies of small molecules with HepG2 cell line, where the samples were only treated with acetonitrile and then diluted with the micellar diluent (demonstrating the reduction of tedious sample preparation requirements for biological samples prior to chemical analysis).