Cortisol: Enemy Number One for Low Carb Diets
Cortisol is released from the adrenal glands to mobilize amino acids from tissues (primarily muscle) to increase the availability of glucose through gluconeogenesis, making cortisol catabolic or muscle-wasting.
In the context of training, cortisol is released during high-intensity, anaerobic exercise to maintain normal glucose levels. The amount of glycogen you've stored directly impacts the release of exercise-induced cortisol. The more glycogen you have stored, the less cortisol is released, and the less glycogen you have, the more cortisol is released.
Intuitively, this gives us reason to suspect that long-term glycogen depletion resulting from long-term low-carb diets may lead to chronically elevated cortisol levels. Low-carb diets also result in an increased exercise-induced cortisol response.
There's evidence that proper nutrient timing could definitely reduce increased exercise-induced cortisol release. Anecdotally, we observe this all the time with successful protocols that manipulate nutrient timing while still being considered low carb.
Center Carbs Around Workouts
In high-intensity, anaerobic exercise, your body relies mainly on glucose from blood glucose, muscle glycogen, hepatic glucose output, and gluconeogenesis for fuel. Your body will also utilize glucose to replenish muscle and liver glycogen post exercise. Fortunately, your body is cheap and thrifty and will utilize the easiest, most available source first and save your muscle tissue for last.
To reduce the need for cortisol production and to keep your body from using amino acids from your muscles as fuel, increase your carb intake at workout time. Eating carbs prior to training (or using a specialized workout drink) will increase blood glucose levels, reducing the amount of cortisol needed to meet energy demands.
You can maintain a low-carb diet (25-30% of your total calories from carbs) by reserving carbs for only workouts (before, during, after) and eating high protein and fat meals the rest of the day. Not only will this timing of carbs suppress cortisol and its catabolic effects, it'll also result in secretion of the anabolic hormone insulin.