Doubly labelled water (DLW) is routinely used to measure energy expenditure and water turnover in free-ranging animals. Standard methods involve capture, blood sampling for baseline measurement, injection with isotopic tracers, captivity for an equilibration period, post-dose blood sampling, release and subsequent recapture for final blood sampling. Single sampling methods that minimise disturbance by reducing capture and handling time have been developed and tested. Sampling faeces rather than blood could further reduce disturbance to study animals in a range of species and study systems. However, the extent to which estimates of metabolic rate derived from blood and faecal samples diverge has not been investigated. We compared isotopic enrichment in blood and faecal samples taken concurrently from captive Southern Pied Babblers Turdoides bicolor. Isotopic enrichment levels in faeces and in blood were used to calculate initial and final ratios of δ 18 O∕δ 2 H for each individual. We then used these ratios to calculate daily energy expenditure (DEE) and directly compared measurements from blood samples with those from faecal samples within individuals. We found that faecal sampling resulted in estimates of DEE that agree with those based on blood sampling. Additionally, we field-tested a faecal sampling protocol with a habituated population of babblers in the southern Kalahari Desert. During the field test, study animals were not captured or handled for either dosing or sampling. Field-testing confirmed the practical feasibility of non-invasive dosing and sampling techniques in free-living animals, and we obtained measurements of DEE that we used to test an a priori prediction that DEE is inversely related to air temperature. Our data show decreasing DEE with increasing air temperature, a pattern consistent with studies testing similar predictions in birds using traditional DLW methods. We demonstrate that faecal samples can substitute for blood when measuring DEE using DLW and provide a method that will allow field-based researchers to obtain sound physiological measurements while minimising handling and removal of study animals from their natural environments. A plain language summary is available for this article.