This paper presents a quantitative investigation into the effect of analyte-additive interactions on analyte migration behavior in capillary electrophoresis (CE) when both 1:1 and 1:2 stoichiometries are present Equations based on the individual capacity factors for each interaction are derived to account for the effect of both first- and second-order equilibria. The analyte migration behavior is described using these equations with a full account of how the microscopic equilibrium constants and microscopic mobilities are combined to give the macroscopic values. The binding isotherms of interactions with both 1:1 and 1:2 stoichiometries are compared with those of a 1:1 stoichiometry. 4,4′-Biphenol and 4-phenylphenol were chosen as analytes that undergo complexation with one and two hydroxypropyl-β-cyclodextrin (HP-β-CD) molecules; phenol was used as an analyte that interacts with only one HP-β-CD molecule. The process of calculating higher order equilibrium constants and complex mobilities from the binding isotherms is demonstrated. The effects of experimental conditions, such as the additive concentration range and the number of data points, on the error in the calculated constants and the ability of the equations to accurately describe the experimental data are discussed. A comparison of the linear transformations of the binding isotherm with respect to their ability to detect higher order equilibria is made, and the advantage of using the capacity factor in CE is illustrated.