What Happens to Glycogen During Ketosis?

December 27, 2025 •

3 min read

During the first few days of a ketogenic diet, the body depletes its stored glycogen, leading to a noticeable drop in weight, primarily from water loss. This depletion is the metabolic trigger that shifts the body into ketosis, a state where it uses fat for fuel instead of carbohydrates.

Quick Summary

The body depletes its glycogen reserves during the initial stages of ketosis as it seeks an alternative fuel source. Gluconeogenesis provides a small but steady supply of glucose for vital organs, while the body becomes adept at using ketones derived from fat for most of its energy needs. Long-term, glycogen levels are maintained through this process.

Key Points

Initial Depletion: Glycogen stores are rapidly used up in the first 24-48 hours of carbohydrate restriction to initiate ketosis.
Water Weight Loss: The initial weight loss on keto is largely due to the release of water that is stored alongside glycogen.
Gluconeogenesis: The liver produces small amounts of glucose from non-carb sources (like amino acids and glycerol) to supply glucose-dependent tissues.
Glycogen Sparing: With keto-adaptation, the body learns to preserve and efficiently use its remaining glycogen stores.
Fuel Source Shift: The body transitions from primarily burning glycogen for energy to using ketones and fat, a state known as metabolic flexibility.
Exercise Adaptation: Keto-adapted athletes show a different fuel utilization pattern, using more fat and sparing glycogen during exercise.

The Initial Depletion Phase

When carbohydrate intake is drastically reduced, as it is on a ketogenic diet, your body first turns to its most readily available energy reserve: glycogen. Glycogen is a chain of glucose molecules stored mainly in the liver and muscles. In a state of carbohydrate restriction, the body's demand for glucose continues, and it begins to break down these glycogen stores through a process called glycogenolysis. This is the phase that kicks off the metabolic shift toward ketosis.

Liver Glycogen: The liver's primary role is to maintain blood glucose levels for the brain and other essential tissues. When blood sugar drops, the liver releases its glycogen to provide glucose. On a keto diet, this reserve is typically exhausted within 24 to 48 hours.
Muscle Glycogen: Muscle glycogen is used locally for energy by the muscles during exercise. This store is also drawn upon but tends to be more resilient and is not completely depleted, especially in resistance-trained individuals.

The Role of Gluconeogenesis

Even in ketosis, some bodily functions and tissues, such as red blood cells and parts of the brain, require a minimal amount of glucose. To meet this need without dietary carbohydrates, the body performs gluconeogenesis (GNG), which literally means 'the making of new sugar'. In this process, the liver uses non-carbohydrate sources—primarily lactate, glycerol, and certain amino acids—to synthesize glucose.

Gluconeogenesis is often misunderstood as a process that burns muscle for fuel. However, the body is highly efficient and uses substrates from dietary protein or fat stores before resorting to breaking down muscle tissue. Furthermore, research has shown that gluconeogenesis can even contribute to replenishing muscle glycogen stores in keto-adapted individuals.

Keto-Adaptation and Glycogen Sparing

As the body becomes keto-adapted over several weeks, it gets better at utilizing ketones for energy. This allows it to preserve its remaining glycogen stores more effectively. Studies have shown that keto-adapted athletes can have similar or even slightly higher muscle glycogen levels compared to those on a high-carb diet, even though their glycogen utilization during exercise is different. This "glycogen-sparing" effect is a key metabolic adaptation that counters the popular myth that a low-carb diet is detrimental to athletic performance.

Glycogen and the Initial Weight Loss

One of the most immediate effects of glycogen depletion is the rapid weight loss experienced by many during the first week of a ketogenic diet. This is primarily water weight. For every gram of glycogen stored, the body holds onto approximately three grams of water. As these glycogen stores are used up, the body expels the associated water, leading to a quick drop on the scale and the phenomenon known as "keto flu" symptoms like dehydration. Electrolyte supplementation is often recommended to combat this initial fluid loss.

Comparing Glycogen in a Keto vs. Standard Diet


Feature	Ketosis (Low-Carb)	Standard Diet (High-Carb)
Initial Glycogen Status	Depleted rapidly to initiate ketosis.	Readily available and consistently refilled.
Long-Term Glycogen Levels	Maintained at lower, but sufficient, levels.	Stores are kept full due to high carb intake.
Energy Source	Primarily ketones and fat, with glucose from GNG.	Primarily glucose from dietary carbohydrates.
Glycogen Utilization	Spared during exercise; used more efficiently.	Main fuel for high-intensity exercise.
Post-Exercise Replenishment	Rely on gluconeogenesis and low-carb intake.	Quick replenishment from dietary carbs.
Body's Metabolic State	Ketone-adapted, metabolically flexible.	Glucose-dependent, less metabolically flexible.

Conclusion

In conclusion, what happens to glycogen during ketosis is a dynamic and adaptive process. Glycogen stores are initially depleted to trigger the metabolic switch to fat-burning. However, the body is intelligent and resilient, using gluconeogenesis to supply glucose to essential organs and developing a glycogen-sparing effect to maintain sufficient levels, particularly in the muscles. Long-term, nutritional ketosis does not deplete glycogen stores indefinitely but rather changes how and when the body uses them, promoting greater metabolic flexibility. This is why concerns about total glycogen depletion and its impact on health and performance are often overstated, especially for keto-adapted individuals.

For more detailed information on ketogenesis and metabolism, the NIH offers a comprehensive resource. For more information, see the NCBI Bookshelf on Ketogenesis.

Frequently Asked Questions

No, you do not completely lose all your glycogen. Liver glycogen is depleted quickly, but muscle glycogen stores are maintained at lower but sufficient levels, especially with regular exercise. The body becomes more efficient at sparing and maintaining them.

The body's liver produces the necessary glucose through a process called gluconeogenesis (GNG), using sources like glycerol from fats and amino acids from protein.

Yes, you can still build muscle on a keto diet. Gluconeogenesis can help replenish muscle glycogen stores, and studies show comparable muscle gains between keto and standard diets, particularly with resistance training.

The 'keto flu' refers to symptoms like headaches and fatigue during the initial phase. It is a side effect of rapid glycogen depletion, which causes water and electrolyte loss as the stored glycogen is used up.

Liver glycogen is typically depleted within 24 to 48 hours of carbohydrate restriction. The speed of depletion can depend on factors like initial stores and activity levels.

Yes, exercise accelerates the initial depletion of glycogen stores, but regular exercise also helps in better preserving and more efficiently utilizing muscle glycogen once keto-adapted.

Yes, glycogen stores can be refilled through gluconeogenesis, particularly muscle glycogen. The body's metabolic adaptation allows it to prioritize storing this new glucose in glycogen rather than burning it immediately.

No, gluconeogenesis is an essential and regulated process that ensures a steady supply of glucose for vital tissues. The body uses ketones for most energy, reducing the demand for glucose and preventing excessive muscle breakdown.