The exact measurement of the temperature in laboratory continuous flow processes is of high importance for many investigations e.g. of heat transfer or reaction kinetics. In particular, miniaturization poses high challenges on temperature measurement due to increased heat transfer. Despite the high relevance of this topic, there are only few publications dealing with accurate inline temperature measurement in flow chemistry and no studies examining the influence of the installation of the temperature sensor on the actual measured temperature. This work deals with inline temperature measurement using a conventional Pt100 sensor with 1.6 mm outer diameter and 20 mm measuring length in a T-piece in a continuous flow reactor on the micro-scale. The issue of heat loss in the T-piece is illustrated in a computational fluid dynamics CFD simulation. The T-piece temperature and the corresponding temperature measured by the Pt100 sensor in an insulated and not insulated T-piece are simulated and compared with experimental data. Moreover, different insert positions and orientations of the Pt100 sensor are simulated and discussed. The extensive CFD simulations demonstrate that using the side-on position of the Pt100 within an insulated T-piece leads to the most precise temperature measurements. Furthermore, the study shows that tilting of the Pt100 inside the T-piece has almost no influence on the temperature measurement as long as the measuring section of the Pt100 is fully inserted. Based on these results, a best practice approach for inline temperature measurement in micro-scale continuous flow reactors is presented for minimal measurement error.