Preheat the oven to 350°F (175°C) and line a 12-cup muffin pan with liners.
Trim the zucchini ends and grate the zucchini; gently squeeze to remove excess moisture if it seems very wet.
In a small bowl, whisk together the coconut flour, almond flour, baking soda, and pumpkin pie spice until evenly combined.
In a large bowl or the bowl of a stand mixer, beat the sugar, Greek yogurt, and eggs until the sugar is incorporated and the mixture is smooth.
Add the dry flour mixture to the wet ingredients a little at a time, mixing on medium speed until just combined.
Fold the shredded zucchini into the batter until evenly distributed.
Spoon the batter into the prepared muffin cups, filling each about three-quarters full to make 12 large muffins.
Bake for 30–35 minutes, or until a toothpick inserted into the center comes out clean or with a few moist crumbs.
Allow the muffins to cool in the pan for 5–10 minutes, then transfer to a wire rack to cool completely.