Preheat the oven to 350 degrees F (175 degrees C). Grease a muffin tin.
Mix oat flour, flax seeds, baking soda, salt, cinnamon, ginger, nutmeg, and allspice in a bowl.
Whisk pumpkin puree, eggs, honey, coconut oil, milk, and vanilla extract together in a separate bowl. Pour in flour mixture and gently stir. Add chocolate chips, oats, and cranberries and fold in.
Divide batter evenly among the muffin cups.
Bake in the preheated oven until a toothpick inserted into the center comes out clean, about 20 minutes.