We examined the hypothesis that accelerating endogenous carbohydrate oxidation exacerbates prolonged exercise-induced reductions in power output at the intensity domain transitions. Eleven trained cyclists undertook assessments of power output at the moderate-to-heavy (first ventilatory threshold [VT1]) and heavy-to-severe transition (three-minute all-out test end-test power [CP3MAOT]) on four occasions: without prior cycling (CON); without prior cycling, but two hours after 500 mg niacin ingestion and with mild heat stress applied locally to the upper legs for two hours prior to assessments (CON+NH); with two hours of prior cycling (EX); and with two hours of prior cycling, 500 mg of pre-exercise niacin ingestion, and mild heat stress applied locally to the upper legs during two hours of prior cycling (EX+NH). Endogenous carbohydrate oxidation was ~19% higher in EX+NH than EX. Power output at the intensity domain transitions were not different between CON and CON+NH. Power output at VT1 was reduced by ~7% in EX vs. CON, and a further ~7% in EX+NH. The lower power output at VT1 in EX and EX+NH was largely attributable to reduced metabolic power, but the larger reduction in power output at VT1 in EX+NH was attributable to effects on metabolic efficiency. CP3MAOT was not different between-trials, and W’ was ~25% lower in EX and EX+NH than CON and CON+NH, with no difference between exercise conditions. These data support a role for endogenous carbohydrate depletion in durability of the moderate-to-heavy but not heavy-to-severe transition during prolonged exercise.