It's not the act of going on long runs, but how your individual body uses fuel as well as your level of fitness that can cause atrophy or muscle wasting, according to exercise physiologist and NASM-certified personal trainer Krissi Williford, MS, from Xcite Fitness.
"Running, depending on your pace and length of the run, will use mostly glycogen from carbohydrates," explained ACE-certified trainer and weight-loss health coach Rachel MacPherson. She went on to say that running for an hour will not burn muscle if you have eaten properly in the hours and days beforehand.
Krissi added that muscle loss when doing longer runs also has to do with how efficient your body is at burning calories. "When you start exercising, you aren't that efficient, especially if you haven't been exercising at all," Krissi said, meaning your body will need more calories for fuel.
Over time, your body adapts as your level of fitness improves. "It's easier for the body to do the work on fewer calories because it is more efficient," Krissi said. So the more your body gets used to these longer runs, the lower the risk of burning muscle, as long as you're eating enough.