Preheat and Prep: Heat your oven to 350°F with the rack in the middle. While it's heating up, line your muffin tin with parchment liners or grease it well with ghee or coconut oil.
Grate and Squeeze: Grate the zucchini using the large holes of a box grater. Transfer the shreds to a clean kitchen towel and squeeze firmly over the sink. You should see a stream of liquid come out. Aim for a texture that holds together when packed but doesn't drip water.
Whisk the Dry: In a medium bowl, whisk together the almond flour, unsweetened cocoa powder, baking soda, cream of tartar, and salt until no clumps remain.
Beat the Wet: In a large bowl, add the coconut sugar, eggs, and vanilla. Use a hand mixer on medium-high to blend for 2 to 3 minutes. The mixture should lighten to a pale, creamy brown and look slightly frothy. This step is important — it helps dissolve the coconut sugar and creates a smooth base.
Fold in the Zucchini: Stir the squeezed zucchini into the bowl of wet ingredients until it's evenly distributed.
Combine Wet and Dry: Add the dry ingredients to the wet. Use a silicone spatula to mix gently until just combined. Be careful not to over-mix, which can make the almond flour release its oils and turn gummy.
Add the Chocolate Chips: Fold in the ½ cup of chocolate chips. Reserve a small handful for the tops.
Fill the Liners: Divide the batter evenly into the 12 liners. Fill each cup until the batter reaches about ¼ inch from the top. Use a cookie scoop for this — it's faster and less messy. Dot the tops with the reserved chocolate chips.
Bake and Rotate: Bake at 350°F for 25 to 30 minutes (start checking at 25), rotating the pan at the halfway mark so they bake evenly. The muffins are done when the tops are golden brown and spring back to a gentle touch, and a toothpick inserted into the middle of the tallest muffin comes out clean.
Cool Completely: Remove the muffins from the oven and immediately transfer them to a wire cooling rack. Let them cool completely before digging in. Cooling sets the crumb perfectly and prevents them from sticking to the liners.