Calorie Breakdown. On average, a plain, medium bagel that's 3.5 inches in diameter contains 270 calories, while a small, 3-inch bagel has just 177 calories. One tablespoon of regular cream cheese has 50 calories, while 1 tablespoon of low-fat cream cheese has just 30 calories. Therefore, a medium bagel with 1 tablespoon of cream cheese contains 320 calories, while a small bagel with 1 tablespoon of low-fat cream cheese contains 207 calories.