Pressure swing adsorption (PSA) assemblies with temperature-based breakthrough detection systems, as well as to hydrogen-generation assemblies and/or fuel cell systems containing the same, and to methods of operating the same. The detection systems are adapted to detect a measured temperature associated with adsorbent in an adsorbent bed of a PSA assembly and to control the operation of at least the PSA assembly responsive at least in part thereto, such as responsive to the relationship between the measured temperature and at least one reference temperature. The reference temperature may include a stored value, a previously measured temperature and/or a temperature measured elsewhere in the PSA assembly. In some embodiments, the reference temperature is associated with adsorbent downstream from the adsorbent from which the measured temperature is detected. In some embodiments, the PSA cycle and/or components thereof are determined at least in part by the relationship between the measured and reference temperatures.