The classic format of the microscale thermophoresis technique (MST) requires the use of disposable glass capillaries. Their total capacity significantly exceeds the volume of the sample used directly in the thermophoretic measurement. An alternative approach that allows for reducing the consumption of sample, reagents and elimination of waste is the use of narrow-bore capillaries, commonly applied in the capillary electrophoresis technique (CE), in combination with injecting sample segment of a reduced length. This article presents the first-ever use of a transparent and flexible narrow-bore capillary for this purpose, which is much easier to handle than a regular non-transparent silica capillary. In this approach, it is possible to perform thermophoretic analysis with a small sample volume, which is delivered to the detection site using pressure-induced flow, or electrophoretically – while simultaneously performing electrophoretic separation. We focused primarily on the former approach, called Transparent Capillary Stop-Flow MicroScale Thermophoresis (TCSF-MST). Its potential was demonstrated in systems presenting the original use of the thermophoresis phenomenon: monitoring the progress of the fluorescent derivatization reaction, determining the critical micellization concentration of a surfactant, and quantitative analysis of fluorophores based on the internal standard method. The obtained results suggest that the new format can be considered an interesting alternative to the traditional MST methodology, and also seems consistent with the idea of "green" and "white" analytical chemistry.