PDF book download! Secrets of the Skinny System, by The NEW Jessica. During gluconeogenesis, the liver (and occasionally the kidneys) turns non-sugar compounds like amino acids (the building blocks of protein), lactate, and glycerol into sugar that the body uses a fuel. When glycogen (your body’s sugar storage) is low, protein intake is high, or the body is under stress then amino acids from your meals and your muscle become one of your main energy sources. If your body continues to convert amino acids into fuel, it can keep you from getting into ketosis. This is why some ketogenic dieters may experience an increase in body fat percentage and a decrease in muscle mass during their first couple weeks on the ketogenic diet. But there is no need to worry. The ketogenic diet will still help reverse common health issues like diabetes and obesity and improve health in many ways. When you start the diet, however, gluconeogenesis will get in the way. In a review of multiple fasting studies, researchers found that it takes between 18 and 24 hours to deplete glycogen stores and more than 2 days after that for the body to shift into ketosis.