As a result of continuous instrumental progress, capillary electrophoresis has become an established separation technique. However, the choice of the suitable capillary inner diameter is sometimes difficult due to different instrumental requirements concerning injection, separation, or detection. To overcome this problem, we assembled two capillaries with different inner diameters, meaning that the inner diameter of the capillary at the injection side was different from that at the detection side. Since this was a rather uncommon approach, we focused on the associated effects in this proof-of-concept study. For the experiments, a non-aqueous model system was used, consisting of an acetonitrile-based background electrolyte and the two ferrocene derivates, ferrocenemethanol and decamethylferrocene. Using capillary flow injection analysis hyphenated to capacitively coupled contactless conductivity detection, it could be shown that fragmented capillaries of the same inner diameter had slightly lower volume flow rates than non-fragmented capillaries. With non-aqueous capillary electrophoresis hyphenated to UV detection, it was found that the coupling of capillaries with different inner diameter had a much stronger effect on the capillary electrophoresis flow than combinations with the same inner diameter. Additionally, if the inner diameter of the second capillary was larger than the inner diameter of the first capillary, a higher theoretical plate number and an increased sensitivity were found. Furthermore, it was found that there was no significant peak tailing introduced by the coupling.