The transient plane source (TPS) technique, also referred as the Hot Disk method, has been widely used due to its ability to measure the thermal properties of an extensive range of materials (solids, liquids, and powder). Recently, it has been recognized that typical Hot Disk sensors can influence TPS results of thermally insulating materials and lead to an overestimation of thermal conductivity. Although improvements have been proposed, they have not yet been implemented in the commercial TPS, leaving researchers with non-standardized modifications or options provided by a commercial Hot Disk apparatus. An empirical study of thermally insulating materials such as extruded polystyrene (XPS) and aerogel blanket is conducted in order to address the factors that affect the reliability of thermal conductivity k obtained using the commercial TPS apparatus. Sensor size, input power, duration of the measurements, applied pressure, and, in the case of anisotropic materials, heat capacity are investigated, and the results are compared with those using a Heat Flow Meter apparatus. The effect of sensor size on the k value is ascribed to heat loss through connecting leads and is more pronounced in smaller sensors and in materials with lower k values. In the case of XPS and aerogel, the effect becomes minimal for sensors with a radius r ≥ 6.4 mm. The low input power yields a high scattering of the results and should be avoided. Applied contact pressure and the tested region of the specimen play an important role in experiments with low-density fibrous materials due to the large percentage of heat being transferred by radiation and the heterogeneous nature of the samples, respectively. Additionally, the sensitivity of anisotropic measurements to the value of the material’s volumetric heat capacity (ρCp) is shown, emphasizing the need for the precise determination.