Contrary to popular belief, exercising on an empty stomach doesn't speed up your metabolism. The problem is that just because you're using more fat as fuel doesn't mean you're actually burning more fat from your body. Burning fat has more to do with your total calorie expenditure, not just the type of energy your body uses for your workout. A routine like mine (exercising first thing in the morning, hours after eating) forces the body to burn fat for fuel.
But taking this approach won't melt the top of your muffin. Instead, the body begins to break down sugars from muscle tissue. These changes in gene expression mean that your body will have a much easier time breaking down stored fat and burning it. At least one other study, published in the National Strength and Conditioning Journal, has shown that burning calories is the same during cardiovascular exercise, whether you eat or not.
Once your carbohydrate stores begin to run out, your body shifts to burning stored fat, but this takes longer to convert into energy. Protein will provide some fuel to your body, but protein doesn't increase your insulin levels as much as carbohydrates will, meaning your body will have fuel, but without reducing fat burning. If you just want to lose fat, your priority is fat oxidation, so you want to go into steady state cardio fasting. When a team of researchers analyzed the effect of four weeks of cardiovascular exercise performed on an empty stomach or on a fed basis, only fasting cardiovascular exercise led to a decrease in the percentage of body fat.
Therefore, after a night without eating, your body could burn a higher percentage of fat by exercising on an empty stomach, as your carbohydrate reserve (your body's preferred energy source) is not readily available. While fasting cardiovascular exercise doesn't affect the total amount of fat you lose, it can increase the amount of fat lost in certain areas of the body. You will burn a higher percentage of fat by exercising on an empty stomach, but only if you do a low-intensity exercise (walking, light cardiovascular exercise). The increase in blood flow makes it easier for the various hormones that trigger the breakdown of stored fat to reach fat cells in the first place.
Your body does not worry about digesting large amounts of food and is able to carry oxygen to the muscles and burn fat. It is the contribution of exercise to a person's total daily energy expenditure (TDEE), including intensity, that affects fat loss. In addition, your body not only burns fat during workouts, it can also burn fat afterwards, a phenomenon known as excessive oxygen consumption after exercise.