Prep the pan and oven. Preheat your oven to 350°F (175°C).
Line a 12-cup muffin tin with paper liners or lightly grease with oil spray to prevent sticking.
Prepare the “apple” bites. Finely chop peeled zucchini or chayote into tiny pieces (about pea-size). Pat dry with paper towels to remove excess moisture. If you have time, sauté them in a dry pan for 2–3 minutes to cook off water.
Let cool.
Mix the dry ingredients. In a large bowl, whisk together 2 cups almond flour, 2 tablespoons coconut flour, 1/2 to 2/3 cup keto sweetener, 2 teaspoons baking powder, 1 1/2 teaspoons cinnamon, 1/4 teaspoon nutmeg, a pinch of allspice or cloves (optional), and 1/2 teaspoon salt.
Combine the wet ingredients. In another bowl, whisk 3 large eggs, 1/3 cup unsweetened almond milk, 1/3 cup melted butter or coconut oil (slightly cooled), 1/3 cup Greek yogurt or sour cream, 1 teaspoon vanilla, and 1 to 1 1/2 teaspoons apple extract.
Bring it together. Pour the wet mixture into the dry ingredients and stir until just combined. Fold in 1 cup of the chopped zucchini or chayote. The batter should be thick but scoopable; add a splash more almond milk if needed.
Portion the batter. Divide evenly among the 12 muffin cups, filling each about 3/4 full.
If using nuts, sprinkle a few on top. For a bakery-style finish, mix a teaspoon of granulated sweetener with a pinch of cinnamon and dust lightly over each muffin.
Bake. Bake for 18–22 minutes, or until the tops are set and a toothpick inserted in the center comes out clean or with a few moist crumbs. Ovens vary, so start checking at 17 minutes.
Cool properly. Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
Keto muffins firm up as they cool, so be patient for best texture.