BACKGROUND: Recent research has demonstrated decreases in resting metabolic rate (RMR), body composition and performance following a period of intensified training in elite athletes, however the underlying mechanisms of change remain unclear. Therefore, the aim of the present study was to investigate how an intensified training period, designed to elicit overreaching, affects RMR, body composition, and performance in trained endurance athletes, and to elucidate underlying mechanisms. METHOD: Thirteen (n = 13) trained male cyclists completed a six-week training program consisting of a "Baseline" week (100% of regular training load), a "Build" week (~120% of Baseline load), two "Loading" weeks (~140, 150% of Baseline load, respectively) and two "Recovery" weeks (~80% of Baseline load). Training comprised of a combination of laboratory based interval sessions and on-road cycling. RMR, body composition, energy intake, appetite, heart rate variability (HRV), cycling performance, biochemical markers and mood responses were assessed at multiple time points throughout the six-week period. Data were analysed using a linear mixed modeling approach. RESULTS: The intensified training period elicited significant decreases in RMR (F(5,123.36) = 12.0947, p = <0.001), body mass (F(2,19.242) = 4.3362, p = 0.03), fat mass (F(2,20.35) = 56.2494, p = <0.001) and HRV (F(2,22.608) = 6.5212, p = 0.005); all of which improved following a period of recovery. A state of overreaching was induced, as identified by a reduction in anaerobic performance (F(5,121.87) = 8.2622, p = <0.001), aerobic performance (F(5,118.26) = 2.766, p = 0.02) and increase in total mood disturbance (F(5, 110.61) = 8.1159, p = <0.001). CONCLUSION: Intensified training periods elicit greater energy demands in trained cyclists, which, if not sufficiently compensated with increased dietary intake, appears to provoke a cascade of metabolic, hormonal and neural responses in an attempt to restore homeostasis and conserve energy. The proactive monitoring of energy intake, power output, mood state, body mass and HRV during intensified training periods may alleviate fatigue and attenuate the observed decrease in RMR, providing more optimal conditions for a positive training adaptation.