The lack of design rules for the design and selection of phase change material (PCM)-based thermal energy storage (TES) systems using heat exchangers is a major impediment to the development and general acceptance of such systems. In order to get to design rules, the thermal storage community must first determine and agree on PCM-based TES performance comparison metrics. This research effort is under way, with studies looking at the impact of size, system's configurations and operating parameters such as temperature and heat transfer fluid (HTF) flow rate. It appears logical that the properties of the selected PCM could play a role in the determination of the sought-after comparison metrics, especially if those metrics take the form of dimensionless numbers. However, no studies have yet been performed looking at the impact of using different PCMs on the performance and the comparability of a define system. This paper presents results of a study performed on a small-scale TES using a coil-and-shell heat exchanger with water as the HTF running in the coil and the PCM filling the rest of the shell volume; the system being filled with 1.14 kg of PCM. Characterization of this TES were performed over a range of initial and final temperatures, both for charging and discharging, where instantaneous power transferred to and from the system was measured through the temperature difference of the HTF between the inlet and outlet of the system. The novelty of this work is the fact that the system was characterized similarly using two different PCMs: OM55 with a melting temperature of 55°C manufactured by PLUSS® and dodecanoic acid with a melting temperature of 43°C bought from Alfa Aesar. Results show that dodecanoic acid appears to provide slightly larger heat transfer rates during both charging and discharging compared to OM55. However, when reducing the data to a comparative metric (the mean heat transfer rate), the analysis shows OM55 with a much greater heat transfer rate during charging. The study leads to important conclusions about experimental approaches to minimize the difficulty of comparing the impact of different PCMs through TES characterization.