Torpor, and its differential expression, is essential to the survival of many mammals and birds. Physiological characteristics of torpor appear to vary between those species that express strict daily heterothermy and those capable of multiday hibernation, but comparisons are complicated by the temperature-dependence of variables. Previous reviews have compared these different torpor strategies by measuring the depth and duration of torpor in multiple species. However, direct comparison of multiple physiological parameters under similar thermal conditions are lacking. Here, we quantified three physiological variables; body temperature, metabolic rate (MR) and heart rate (HR) of two small heterothermic bats (daily heterotherm Syconycteris australis, and hibernator Nyctophilus gouldi) under comparable thermal conditions and torpor bout durations. When normothermic and resting both MR and HR were similar for the two species. However, during torpor the minimum HR was more than fivefold higher, and minimum MR was 6.5-fold higher for the daily heterotherm than for the hibernator at the same subcutaneous Tb (16 ± 0.5 °C). The data show that the degree of heterothermy defined using Tb is not necessarily a precise proxy for physiological capacity during torpor in these bats and is unlikely to reveal accurate energy budgets. Our study provides evidence supporting a distinction between daily torpor in a daily heterotherm and short term torpor in a hibernator, at least within the Chiroptera with regard to these physiological variables. This exists even when individuals display the same degree of Tb reduction, which has clear implications for the modelling of their energy expenditure.