Preheat your oven to 375°F (190°C). Grease a standard muffin pan to prevent sticking. Set the pan aside while you prepare the batter.
In a small bowl, combine the coconut flour, almond flour, ground cinnamon, pumpkin pie spice blend, baking soda, baking powder, and fine sea salt. Whisk to evenly distribute the spices and leavening agents throughout the flour mixture, then set aside.
In a blender or food processor fitted with an 'S' blade, combine the finely shredded zucchini (unpeeled), canned pumpkin puree, coconut sugar, and melted coconut oil. Blend or process until the mixture is smooth with the zucchini well incorporated. This helps give the muffins a moist crumb without visible bits of vegetable. I find grating the zucchini very finely makes for the best texture.
Add the pure vanilla extract and apple cider vinegar to the blended wet mixture and blend until just combined. Next, add the dry ingredient mixture from Step 2 and blend or process again until everything is well combined, creating a thick, uniform batter.
Add all four large eggs to the batter at once. Blend or process until just combined, being careful not to over-mix. This will help the muffins stay light and fluffy.
Remove the blade from the food processor or pour the batter into a mixing bowl. Gently fold in the chocolate chips (or cinnamon-flavored chips) by hand. Scoop 1/4 cup portions of batter into each well of the greased muffin pan prepared in Step 1. I like to keep a few extra chips to sprinkle on top if I want extra chocolatey muffins.
Place the muffin pan in the preheated oven and bake for 20-25 minutes, or until a toothpick inserted in the center of a muffin comes out clean. Allow them to cool in the pan for a few minutes before transferring to a wire rack to cool completely. For the best texture, I recommend letting the muffins cool almost fully before enjoying—this helps them set properly.