Calorie discrepancy?

If it's subtracting calories, then you aren't meeting the maintenance calorie burn MFP has calculated for you at that activity level

MFP expects you to burn X calories per day based on your stats & stated activity level. It assumes every hour is the same, or that you will burn X/24 each hour. In reality you burn less some hours and more others.

Example: if your expected burn per day is 2400 (its an easy # for this example) then MFP thinks you'll burn 100/hr.

When you use a device that estimates your actually calorie burn and sync it to MFP, MFP gets your actual burn from the device, estimates how much you'll burn (in this example at the rate of 100/hour) to see where you'll end the day. If you're behind schedule it deducts calories. If you're ahead, it adds calories.

Unless you're active in the wee morning hours, you'll always start off in the negative. Here is why:

MFP thinks you're going to burn 100 every hour. But perhaps your BMR is only 80, and you wake up at 6am. From midnight-6am, because you were sleeping, you only get credit for 80 x 6 hours = 480. You're behind by 120 because MFP thinks you should be at 600 by 6am. The next hour perhaps you're doing misc. stuff around the house like shower & get dressed & breakfast, not exercising, but you are moving. Perhaps you burn 90. Now you're at 480 + 90 or 570. You're supposed to be at 700, so you're down by 130. But perhaps you go for a morning jog from 7am-8am and burn 350. So your device says you're at 570 + 350 or 920. Its 8am, MFP expected 800, so you're ahead by 120.

MFP does those sort of calculations every time you sync your device. So the + or - will change as the day goes on.

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Note: if your device does NOT estimate calories burned, then MFP is using the # of steps and estimating your actual burn based on # of steps. Then comparing it to your stated level.

It does the same thing with FitBit and I find it rather confusing because you never really know how many exercise calories you'll have by end of day. I don't usually eat back exercise cals as a result, I just consider them as a bonus to my deficit.