Due to its high efficiency, selectivity, and sensitivity, CE-ESI/MS has evolved as an efficient technique for the drugs and metabolites analysis in biological matrices. However, a sample preparation is mandatory prior to CE-ESI/MS analysis. To achieve fast and simplified sample preparation of plasma samples, protein precipitation (PP) and liquid-liquid extraction (LLE) were used with two injection techniques: hydrodynamic (HD) and electrokinetic (EK) injection. CE-ESI/MS analyses of pharmaceutical compounds and amphetamine derivatives were developed. Detection limits of 1 ppm were reached with PP and HID injection whereas 1 ppb was detected when samples were prepared with LLE and injected by EK. Same experiments were performed for stereoselective determinations in partial-filling mode and detection limits achieved were equivalent to conventional analysis (0.5 ppb per enantiomer). When complex matrices are analyzed, MS signal suppression or enhancement effects are generally not reproducible and could compromise results with ESI. Therefore, matrix effect was investigated in CE-ESI/MS with a commercially available coaxial sheath-liquid ESI interface used as postcapillary infusion system to determine MS signal alterations. Matrix effects were differentially evidenced according to the selected sample preparation. With PP, signal suppression was observed out of the analyses migration window, while for LLE no relevant matrix effect occurred in all experiments.