Make It Now:

1. Preheat oven to 350°F. Grease two 12-cup muffin tins or line them with paper liners. 
2. In a large mixing bowl, combine the flour, flax, sugar, baking soda, baking powder, cinnamon, and salt.
3. In a smaller bowl, whisk together the pumpkin puree, oil, applesauce, eggs, and vanilla extract.
4. Stir wet mixture into dry ingredients; mix just until combined (do not over mix). 
5. Stir in the chocolate chips.
6. Spoon the batter into the prepared muffin tins until each one is almost full. 
7. Bake in the preheated oven until a toothpick inserted in the center of a muffin comes out clean, about 20-22 minutes for two pans (or 18-20 for one). Note: Silicone pans will take a few minutes longer to bake. To check for doneness, insert a tooth pick and if it comes out clean then muffins are done. (Freezing instructions begin here.)
8. Let cool on a cooling rack for 10 minutes in the tin. Remove muffins and place on the cooling rack a bit longer.

Freeze For Later: Bake muffins as directed in recipe. Let cool completely. Then place in a gallon-sized freezer bag or container, seal tightly, and store for up to 3 months. 

Prepare From Frozen: Thaw muffins in the refrigerator or warm in the microwave.