Background While recent studies indicate that in humans fat-free mass (FFM) is closely associated with energy intake (EI) when in energy balance, associations between fat mass (FM) and EI are inconsistent. Objectives The present study used a cross-sectional design to examine the indirect and direct effects of FFM, FM and resting metabolic rate (RMR) on EI in individuals at or close to energy balance. Methods Data for 242 individuals (114 males; 128 females; BMI = 25.7 ± 4.9 kg/m2) were collated from the non-intervention baseline conditions of five studies employing common measures of body composition (air-displacement plethysmography), RMR (indirect calorimetry) and psychometric measures of eating behaviours (Dutch Eating Behaviour Questionnaire). Daily EI (weighed dietary records) and energy expenditure (flex heart rate) were measured for 6–7 days. Sub-analyses were conducted in 71 individuals who had additional measures of body composition (dual-energy X-ray absorptiometry) and fasting glucose, insulin and leptin. Results After adjusting for age, sex and study, linear regression and mediation analyses indicated that the effect of FFM on EI was mediated by RMR (P < 0.05). FM also independently predicted EI, with path analysis indicating a positive indirect association (mediated by RMR; P < 0.05), and a stronger direct negative association (P < 0.05). Leptin, insulin and insulin resistance failed to predict EI, but cognitive restraint was a determinant of EI and partially mediated the association between FM and EI (P < 0.05). Conclusions While the association between FFM and EI was mediated by RMR, FM influenced EI via two separate and opposing pathways; an indirect ‘excitatory’ effect (again, mediated by RMR), and a stronger direct ‘inhibitory’ effect. Psychological factors such as cognitive restraint remain robust predictors of EI when considered alongside physiological determinants of EI, and indeed, have the potential to play a mediating role in the overall expression of EI.