Can run 6 km without getting out of breath but cannot get rid of muffin top?

Can run 6 km without getting out of breath but cannot get rid of muffin top?
why am I not thinner?
I walk or bike to work everyday (a 3km round trip) and everywhere I need to get, I run at least 2km everyday, and go hiking in the weekends.i eat yoghurt for breakfast, fruit and walnuts for lunch and vegis and chickpeas for dinner. about once a week I crack and eat a packet of biscuits but the other 6 days a week I'm eating well under 1000calories per day...i hardly drink,
i work with a girl who is 3 dress sizes smaller than me who has never been to the gym and doesn't even own sneakers.
im fitter than most people I know but my thighs still look wobblier than anyone elses and disgusting. WHY? its so frustrating!