Glycogen Depletion and Fat Oxidation for Ultrarunners: What Powers Long Runs, When You Bonk, and How Training Changes the Mix

Glycogen depletion and fat oxidation matter to ultrarunners because they shape how long you can hold a given effort, how stable your pace feels late in a run, and why a day can fall apart even when your legs seemed fine an hour earlier.

One of the most persistent misunderstandings in endurance training is that long races are powered mostly by fat, so carbohydrate becomes secondary. The truth is more useful and more complicated. Ultrarunners do rely heavily on fat oxidation, which means burning fat to produce energy. But they also depend on carbohydrate, stored in the body as glycogen, especially when the terrain steepens, the pace rises, the temperature climbs, or fatigue starts to accumulate.

If you understand how those two fuel systems interact, several common experiences start to make sense. You understand why an easy long run can feel steady for hours but a slightly faster effort suddenly becomes fragile. You understand why fueling mistakes may not show up immediately. You understand why fitness can improve your ability to use fat without making glycogen irrelevant. And you understand why bonking is not simply running out of calories.

Glycogen is the stored form of carbohydrate. Most of it is stored in skeletal muscle and the liver. Muscle glycogen is used locally by the working muscles. Liver glycogen helps maintain blood glucose, which is the glucose circulating in your bloodstream and supplying tissues such as the brain. Both matter during a long run, but in different ways. When muscle glycogen falls, producing force at a given pace becomes harder. When liver glycogen falls and blood glucose drops, effort can suddenly feel mentally and physically worse, even if your pace has not changed much.

Fat oxidation is the process of breaking down fatty acids to generate usable energy in the form of ATP, adenosine triphosphate, the immediate energy currency of muscle contraction. Fat stores are large, even in lean athletes. Glycogen stores are limited. That basic contrast is why so much endurance advice talks about teaching the body to burn more fat. The logic is sound up to a point. If you can do more work aerobically while sparing glycogen, you are better equipped for long events. But the phrase sparing glycogen is often used too loosely, as if a runner can avoid meaningful carbohydrate dependence altogether. That is not how endurance physiology works.

The central issue is rate, not just supply. Fat can provide a large amount of total energy, but it provides it more slowly than carbohydrate. Oxidizing fat requires more oxygen per unit of ATP produced and involves a longer series of metabolic steps than using carbohydrate. At lower intensities, that slower system is good enough. At higher intensities, it is not. As exercise intensity rises, carbohydrate becomes increasingly important because it can support faster ATP production. That is why a runner can hike steadily uphill for hours with fat carrying a large share of the load, but cannot surge repeatedly, climb hard, or race near threshold on fat alone.

This is where intensity matters more than race distance. Many runners assume that because an ultra is long, it is therefore mainly a fat-burning event in a practical sense. But ultras are not run at one fixed metabolic setting. A mountain ultra may include steep hiking, runnable flats, technical descents, aid station stops, altitude, heat, and moments of overpacing. Each of those shifts changes fuel use. The body is always using a mixture of carbohydrate and fat. The proportion changes with intensity, training status, nutrition, and environment.

At easier intensities, especially below the first ventilatory threshold, trained endurance athletes tend to derive a larger share of energy from fat. Even so, they still burn a lot of carbohydrate at low efforts, which is why what feels like an endurance limit is often a fueling limit. As intensity rises toward marathon effort, tempo effort, or threshold, carbohydrate contributes more. That does not mean fat use shuts off. It means carbohydrate takes over a larger share because the demand for rapid energy delivery rises. This one reason critical speed for trail and ultra runners is useful conceptually even for athletes focused on long races. The closer you get to the upper end of sustainable aerobic work, the less room there is to rely primarily on fat.

Training changes this picture in several ways. Endurance training increases mitochondrial density, which means more of the machinery inside muscle cells that supports aerobic energy production. It increases capillary density, improving oxygen delivery to muscle. It also increases the activity of enzymes involved in fat oxidation and improves the ability to transport fatty acids into the mitochondria. Taken together, those changes let trained athletes do more work aerobically at a given pace and use a higher absolute amount of fat than less trained athletes.

That phrase, higher absolute amount, matters. A trained ultrarunner may burn more fat per hour than a novice and still use plenty of carbohydrate. Both can be true at once. This is where some popular discussions become misleading. If a runner improves fat oxidation, that does not mean carbohydrate stops mattering. It often means the runner can preserve glycogen a bit better at a moderate effort, delay carbohydrate depletion, and hold a steadier output over time. That is valuable, but it is not freedom from fueling.

Glycogen depletion is also not an all-or-nothing event. Runners often picture it as a fuel tank hitting empty. In reality, performance usually degrades before glycogen stores are completely exhausted. Some muscle fibers may be more depleted than others. Liver glycogen may be low enough to destabilize blood glucose. Central nervous system drive may drop as the brain perceives rising metabolic strain. Perceived effort climbs. Pace that felt smooth now feels forced. Coordination can worsen. Decision-making may get sloppy. This cluster of symptoms is what many runners call bonking or hitting the wall.

Researchers have studied this most closely in marathon and cycling settings, where the role of carbohydrate depletion is well established. In ultras, the picture is broader because pacing is slower, terrain is variable, and muscle damage, heat stress, hydration problems, and sleep loss can all contribute. But glycogen depletion still matters. It just interacts with more other problems. A runner late in a 100K may not slow only because carbohydrate is low. They may also be managing eccentric muscle damage from descents, rising core temperature, and general fatigue. The reason the slowdown feels so dramatic is that each stressor makes the others harder to absorb.

This interaction helps explain why fueling and pacing are inseparable. If you run too hard early, you increase carbohydrate use and deplete glycogen faster. If you underfuel while doing that, you magnify the problem. If the race is hot, cardiac drift raises cardiovascular strain, often pushing heart rate up at the same pace and making the effort more carbohydrate costly. The body never experiences these factors in isolation.

Liver glycogen deserves more attention than it usually gets in runner conversations. Muscle glycogen supports the local work of running. Liver glycogen supports blood glucose between feedings and during exercise. When liver glycogen becomes severely reduced, blood glucose regulation gets harder. The brain is highly sensitive to that change. You may feel foggy, irritable, shaky, uncoordinated, or unable to tolerate an effort that was manageable earlier. This is one reason a runner can still be moving but feel strangely empty and detached. The problem is not merely tired legs.

So what does fat adaptation actually mean in practical terms? Properly used, it means training that improves your ability to oxidize fat at submaximal intensities, preserve carbohydrate better at those same intensities, and maintain a given pace with less metabolic strain. High-volume easy running is the main driver. Long runs matter because they extend time spent doing aerobic work and force repeated exposure to steady energy demand. Back-to-back long days can also build resistance to late-race fatigue, though they need to be placed carefully. The foundation is still consistent aerobic training, not special tricks.

Nutritional strategies can shift substrate use too. Training with low carbohydrate availability, sometimes called training low, can increase signaling pathways associated with mitochondrial adaptation and may increase the muscle's tendency to oxidize fat. But this area is often oversold. For most ultrarunners, the risks outweigh the benefits. Training quality drops, the low-fuel state adds stress on top of the training itself, and combined with heavy training it can lead to low energy availability, with lower performance and higher injury risk. Easy running, which is most of an ultrarunner's training, is already the best way to train fat burning. For ultrarunners, the wrong lesson is to perform all key sessions underfueled. Workouts that aim to improve quality, threshold, climbing power, or race-specific output usually need carbohydrate support. Using low-carbohydrate availability too often can compromise the very training adaptations you want.

There is a similar problem with the idea that ketogenic or very low-carbohydrate diets are the best answer for long-distance performance. Such diets can raise fat oxidation substantially. That part is real. But higher fat oxidation does not automatically improve race performance. In many studies, especially when performance requires moderate to high intensities, economy can worsen because fat oxidation uses more oxygen for the same external work. In simple terms, you may become better at burning fat but less efficient at moving fast enough to race well. For some slower, steady efforts that tradeoff may be manageable. For competitive ultrarunning on varied terrain, it often becomes limiting.

This is why elite and well-coached amateur ultrarunners usually aim for metabolic flexibility rather than one-fuel purity. Metabolic flexibility means being able to use a lot of fat at easy and moderate intensities while still accessing carbohydrate well when the course or race demands it. You want the diesel engine and the ability to press the accelerator. You want to spare glycogen when you can, not pretend you no longer need it.

Fueling during long training runs and races works within that same framework. Taking in carbohydrate during exercise does not shut off fat burning. It helps preserve blood glucose, reduce the rate of liver glycogen depletion, and support the higher-energy moments that naturally happen in real races. The right amount depends on duration, intensity, and gut tolerance, but there are useful starting points. Easy runs under an hour need no carbohydrate. Easy runs of one to two hours do well with 45 to 60 grams per hour, and easy runs over two hours with 60 to 75. Long trail runs that mix easy and moderate running, and harder sessions over 90 minutes, usually call for 75 to 90 grams per hour. In a race, use what worked in those sessions, and drop toward 60 to 75 grams per hour when the effort falls or the event goes past about 15 hours. Practicing that intake in training matters because the gut is trainable. A runner who only fuels aggressively on race day often discovers that their intestine objects as strongly as their legs. If you want help reviewing how your own long runs are going, you can ask the coach about your training and get feedback grounded in what actually happened in your recent sessions.

This also clarifies why two long runs of the same duration can have very different physiological costs. Consider two four-hour runs. In the first, the runner moves easily on rolling trails, keeps the climbs controlled, and fuels steadily. In the second, the runner chases faster partners, surges every runnable section, underfuels for two hours, and finishes depleted. Both were four hours, but the second consumed glycogen faster, imposed more stress, and probably demanded more recovery. Duration alone did not define the cost. Fuel use and intensity distribution did.

Muscle glycogen also affects pacing in a more local way than many runners realize. Different muscle fibers are recruited depending on force demands, terrain, and fatigue. Hard climbing, running downhill, and technical stabilization can all alter which fibers are carrying the load. Some fibers can become relatively depleted while others are less affected. That uneven depletion may be one reason a runner feels fine on flats but suddenly loses pop on climbs, or can still jog but cannot respond to changes in grade. Whole-body energy status matters, but local glycogen availability matters too.

Another important point is that feeling hungry is not a reliable indicator of carbohydrate need during long exercise. Appetite often lags behind physiological demand, especially in heat or at altitude. By the time a runner feels obviously depleted, performance may already be sliding. This is why race fueling works better when it is planned and repeated than when it is left to preference in the moment.

For training decisions, the practical lessons are straightforward. Build the aerobic base that improves fat oxidation through lots of sustainable easy running. Use long runs to extend durability and practice fueling, not to stage repeated depletion experiments. Support high-quality sessions with enough carbohydrate to hit the intended purpose. Do not use fasted or low-carbohydrate sessions as a strategy. The one limited exception is an easy run of up to about two and a half hours without carbohydrate, and only for men; women should not underfuel. Pace long races conservatively enough that your carbohydrate demand matches what your body stores and what your gut can absorb. When a runner fades badly late, ask about pacing, fueling, heat, terrain, and cumulative fatigue together, because glycogen depletion is usually part of a system failure, not a solo villain. Having an evaluation of every workout can make those patterns easier to spot before they turn into a bigger problem.

For an ultrarunner, the goal is not to become a pure fat burner. The goal is to become the kind of athlete who can move for a long time at a useful speed, preserve glycogen when the course allows it, take in carbohydrate well enough to protect performance, and still have access to higher output when the race asks for it.

Written by Wade Wegner. Train Ultra is a private AI coach that reads every workout from Garmin, COROS, Apple Health, or Health Connect. Try it free.