•Vitamin B6 and Mg were simultaneously determined by CE-C4D.•Vitamin B6 and Mg peaks were well separated within < 10 min.•A simple and reliable method was developed for pharmaceutical/nutraceutical samples.•Single-run CE-C4D analysis can replace HPLC and ICP-OES conventional methods.•Acceptable agreement between measured/label claim contents was achieved. Vitamins and minerals are usually incorporated in pharmaceutical and nutraceutical products, but a simple, rapid, and inexpensive analytical method for their simultaneous determination is still lacking. In this study, we developed a quantification method for pyridoxine (vitamin B6) and magnesium (Mg) by using purpose-made capillary electrophoresis with capacitively coupled contactless conductivity detection (CE-C4D) instrument. Main analytical conditions include: fused silica capillary (total length 55 cm, effective length 40 cm, inner diameter 50 μm); background electrolyte consisted of 10 mM L-arginine/acetic acid (pH 5) with 20% acetonitrile; separation voltage + 20 kV; hydrodynamic injection (siphoning at 20 cm in 25 s). Detection limits of vitamin B6 and Mg were 1 and 0.1 mg/L, respectively. Good linearity (R2 > 0.999) was observed for vitamin B6 and Mg calibration curves over concentration ranges of 3–100 and 0.3–200 mg/L, respectively. The method was applied to analyze vitamin B6 and Mg in several pharmaceutical and nutraceutical samples. The analytical results obtained by our method were in good agreement with reference methods (i.e., HPLC for vitamin B6 and ICP-OES for Mg). High-efficient and low-cost CE-C4D method can accordingly serve as a promising tool for concurrent analysis of inorganic and organic species in pharmaceutical and nutraceutical analysis.