If your pecan pie came out a bit runny, here are a few reasons why that may have happened, and some ways you can fix it next time. First, it might be underbaked. Check for doneness with the tips above to make sure that it's baked properly.  Maybe you cooked at the wrong oven temperature. Some ovens run hot or cold so make sure to calibrate your oven with an oven thermometer to make sure that it's at the right temperature. Make sure you used the right pie plate. Never use a deep dish for this recipe because the extra depth takes too long to cook.  The filling should only be about 1-inch deep.