Preheat Oven & Prepare Muffin Tins if baking right away: Preheat your oven to 350°F (175°C). Line 18-20 muffin tin cups with paper liners or grease them thoroughly.
Prepare Zucchini: Wash the zucchini, trim off the ends, and shred it using the large holes of a box grater. You'll want about 1.5 cups firmly but not overly packed. Set aside. Do not squeeze out the moisture unless your zucchini is unusually large/wet and you see a lot of standing water; the moisture is beneficial here.
Combine Dry Ingredients: In a large mixing bowl, whisk together the flour (1 3/4 cups or 230g, einkorn or all-purpose), granulated sugar, cocoa powder, and salt.
If baking right away: Add the baking soda now.
If long fermenting: Do NOT add the baking soda yet. You'll add it after fermentation. Make a well in the center of the dry ingredients. DO NOT ADD mini chocolate chips till after fermenting.
Add Wet Ingredients: To the well in the dry ingredients, add the sourdough starter, eggs, applesauce, zucchini and oil.
Mix Batter: Stir gently with a wooden spoon or silicone spatula until just combined into a thick batter. Do not overmix; overmixing can lead to tough muffins. A few streaks of flour are perfectly fine.
Optional Long Fermentation:
Cover the bowl of batter with plastic wrap.
Place in the refrigerator for at least 4 hours, or preferably overnight (up to 12-18 hours). This allows the sourdough to work its magic, improving flavor and digestibility.
After fermentation: Remove from the fridge.
Fold Chocolate Chips: Gently fold the chocolate chips into the batter until evenly distributed. Be careful not to overmix.
Fill Muffin Tins: Divide the thick batter evenly among the prepared muffin cups, filling each approximately 3/4 full. The batter will be thick, which is normal and helps create a domed muffin top.
Make the Chocolate Streusel Topping (if using): In a separate small bowl, combine the cold cubed butter, granulated sugar, flour, cocoa powder, and optional cinnamon. Use an electric mixer, pastry cutter, or your fingertips to cut the butter into the dry ingredients until it forms coarse crumbles.
Top Muffins & Bake: Sprinkle about 1-2 tablespoons of the chocolate streusel topping over each muffin (if using). Bake in the preheated oven for 20-25 minutes, or until a wooden skewer or toothpick inserted into the center of a muffin comes out clean or with only a few moist crumbs attached. Do not overbake, as this can dry out the muffins. Zucchini will release moisture as it bakes, contributing to the moist texture.
Cool: Let the muffins cool in the muffin tins for a few minutes before transferring them to a wire rack to cool completely.