This article elucidates the practical impact of the complexation of buffer constituents with complexation agents on electrophoretic results, namely, complexation constant determination, system peak development, and proper separation of analytes. Several common buffers, which were selected based on the pH study in Part I of this paper series (Riesová, M.; Svobodová, J.; Tošner, Z.; Beneš, M.; Tesařová, E.; Gaš, B. Anal. Chem., 2013, DOI: 10.1021/ac4013804); e.g., CHES, MES, MOPS, Tricine were used to demonstrate behavior of such complex separation systems. We show that the value of a complexation constant determined in the interacting buffers environment depends not only on the analyte and complexation agent but it is also substantially affected by the type and concentration of buffer constituents. As a result, the complexation parameters determined in the interacting buffers cannot be regarded as thermodynamic ones and may provide misleading information about the strength of complexation of the compound of interest. We also demonstrate that the development of system peaks in interacting buffer systems significantly differs from the behavior known for noncomplexing systems, as the mobility of system peaks depends on the concentration and type of neutral complexation agent. Finally, we show that the use of interacting buffers can totally ruin the results of electrophoretic separation because the buffer properties change as the consequence of the buffer constituents' complexation. As a general conclusion, the interaction of buffer constituents with the complexation agent should always be considered in any method development procedures.