Is this because the muscle reserves of carbohydrates are low to zero in the morning and therefore the cardio hits only the fat?
It is often thought that there is no best time of day to train for fat loss; that all times are basically equal. This is untrue.
Exercising first thing in the morning BEFORE you eat or drink anything (except water) can result in greater fat loss than exercising at any other time in the day.
The reason for this is that your blood sugar (your body's quick source of energy) is at its lowest point when you wake up in the morning because you've been fasting for 6 or more hours. With little blood sugar available to fuel your muscles, your fat will be mobilized and burned to supply the energy needed to exercise.
If you find that you can't train first thing in the morning, you can still take advantage of the fasting state. Simply train after a longer period of not eating (3-4 hours or more).
For example, if you get home from work and haven't eaten anything since lunch, you are most likely in a fasting state. Exercise now and you will get better results.
If you really want to lose weight fast, with both methods, be sure not to eat anything before you exercise, or what you eat is what will be burned for energy, not your bodyfat.
The only exception to this is protein.
If you're concerned that you may burn up muscle tissue while training (which is a possibility), take a protein shake (only protein) immediately upon waking. This will help preserve muscle tissue.
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