Accelerometry has been widely used to estimate energy expenditure in a broad array of terrestrial and aquatic species. However, a recent reappraisal of the method showed that relationships between dynamic body acceleration (DBA) and energy expenditure weaken as the proportion of non-mechanical costs increases. Aquatic air breathing species often exemplify this pattern, as buoyancy, thermoregulation and other physiological mechanisms disproportionately affect oxygen consumption during dives. Combining biologging with the doubly labelled water method, we simultaneously recorded daily energy expenditure (DEE) and triaxial acceleration in one of the world's smallest wing-propelled breath-hold divers, the dovekie (Alle alle). These data were used to estimate the activity-specific costs of flying and diving and to test whether overall dynamic body acceleration (ODBA) is a reliable predictor of DEE in this abundant seabird. Average DEE for chick-rearing dovekies was 604±119 kJ day−1 across both sampling years. Despite recording lower stroke frequencies for diving than for flying (in line with allometric predictions for auks), dive costs were estimated to surpass flight costs in our sample of birds (flying: 7.24× basal metabolic rate, BMR; diving: 9.37× BMR). As expected, ODBA was not an effective predictor of DEE in this species. However, accelerometer-derived time budgets did accurately estimate DEE in dovekies. This work represents an empirical example of how the apparent energetic costs of buoyancy and thermoregulation limit the effectiveness of ODBA as the sole predictor of overall energy expenditure in small shallow-diving endotherms.