Abstract Standard metabolic rate (SMR) is both a highly informative and variable trait. Variation in SMR stems not only from diverse intrinsic and extrinsic factors, but also from the use of diverse methods for metabolic measurements. We measured CO2 production (V˙CO2) and oxygen consumption rates (V˙O2) using two flow-through respirometry modes, continuous and intermittent (stop-flow), to evaluate their potential contribution to SMR variation in Alpine newts, Ichthyosaura alpestris. Both respirometry modes yielded similar and repeatable V˙CO2 values. Although V˙O2 was highly repeatable, continuous respirometry produced lower V˙O2 than the intermittent method. During intermittent measurements, the total number of activity bouts was higher than during continuous respirometry trials. Statistical correction for disparate activity levels minimized variation in oxygen consumption between respirometry modes. We conclude that use of either method of flow-through respirometry, if properly applied, introduced less noise to SMR estimates than a variation in activity levels.