I’m excited to share my Chocolate Zucchini Muffins made with whole wheat, grated zucchini, maple syrup and applesauce to cut back on added sugar, and studded with chocolate chips for a naturally sweet option.

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I kept wanting something unexpectedly rich but not trashy, so I wrote down a version I actually make on repeat. These Healthy Chocolate Zucchini Muffins read like a cheat code: moist, not cloying, and studded with dark chocolate chips that melt into pockets of intense flavor.

I used grated zucchini for a sneaky vegetable boost, and yeah sometimes I overdo the chocolate but you can control it. If you like slight surprises in a snack, this will make you curious about how something so wholesome still feels like indulgence.

Try one warm and tell me if it fooled you.

Ingredients

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Whole wheat flour: add fiber, iron and nutty flavor, makes muffins more filling and hearty.
Unsweetened cocoa powder: brings chocolate flavor and depth, antioxidants, very low sugar on its own.
Zucchini: adds moisture without extra fat, gives vitamins and subtle veggie sweetness and texture.
Eggs: provide protein, structure and help muffins rise, theyre keep crumb tender and rich.
Pure maple syrup: natural sweetener with minerals, less processed than refined sugar and adds depth.
Unsweetened applesauce: adds moisture and fiber, cuts fat while keeping sweetness mild and natural tang.
Dark chocolate chips: bittersweet chocolate adds rich flavor, some antioxidants, still contains sugar and indulgence.

Ingredient Quantities

1 3/4 cups whole wheat pastry flour or regular whole wheat flour

1/2 cup unsweetened cocoa powder

1 teaspoon baking powder

1/2 teaspoon baking soda

1/2 teaspoon fine sea salt

1/2 teaspoon ground cinnamon optional

2 large eggs

1/3 cup pure maple syrup

1/2 cup unsweetened applesauce

1/4 cup neutral oil (canola, vegetable or melted coconut oil)

1 teaspoon vanilla extract

1 1/2 cups grated zucchini about 1 medium zucchini

1/2 cup dark chocolate chips or chopped dark chocolate

How to Make this

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1. Preheat oven to 350F (175C) and line a 12-cup muffin tin with liners or lightly oil the cups.

2. Grate about 1 medium zucchini to get roughly 1 1/2 cups, then squeeze out some of the excess water in a clean towel or cheesecloth — you want it moist not dripping.

3. In a large bowl whisk together 1 3/4 cups whole wheat pastry flour (or regular whole wheat flour), 1/2 cup unsweetened cocoa powder, 1 teaspoon baking powder, 1/2 teaspoon baking soda, 1/2 teaspoon fine sea salt and 1/2 teaspoon ground cinnamon if using.

4. In the same bowl add the wet ingredients: 2 large eggs, 1/3 cup pure maple syrup, 1/2 cup unsweetened applesauce, 1/4 cup neutral oil (canola, vegetable or melted coconut oil) and 1 teaspoon vanilla extract. Stir gently until just combined, don’t overmix.

5. Fold in the grated zucchini and 1/2 cup dark chocolate chips (or chopped dark chocolate). Tip: toss the chips with a teaspoon of flour first so they don’t all sink to the bottom.

6. Scoop batter into the prepared muffin tin, filling each cup about 3/4 full. If you like, press a few extra chips on top for looks.

7. Bake for 18 to 22 minutes, or until a toothpick inserted in the center comes out with a few moist crumbs but not wet batter. Oven temps vary so start checking at 18 minutes.

8. Let muffins cool in the tin for 5 to 10 minutes, then transfer to a wire rack to finish cooling so they don’t get soggy.

9. Store cooled muffins in an airtight container at room temperature for 2 to 3 days or freeze for longer. Reheat briefly in the microwave to revive that just-baked feel.

Equipment Needed

1. 12-cup muffin tin (paper liners or lightly oil the cups)
2. Box grater or food processor with grater disc (for about 1 medium zucchini)
3. Clean kitchen towel or cheesecloth to squeeze out excess zucchini water, yes really dont skip this
4. Large mixing bowl
5. Whisk and rubber spatula (whisk for mixing, spatula to fold and scrape)
6. Measuring cups and spoons
7. Ice cream scoop or large spoon to portion batter so muffins bake evenly
8. Small bowl to toss chocolate chips with a teaspoon of flour so they dont all sink
9. Wire cooling rack, toothpick to test doneness, and oven mitts for safe handling

FAQ

Q: Can I use regular whole wheat flour or all-purpose instead of whole wheat pastry flour? A: Yes. Whole wheat pastry gives a lighter texture, but regular whole wheat works 1:1 and will be a bit denser. All-purpose also works 1:1 and makes them slightly fluffier. Tip: spoon flour into the cup and level it, dont pack it down.

Q: Do I need to peel or squeeze the zucchini? A: No peel needed, the skin is fine and adds color. You also dont need to squeeze out the liquid unless the zucchini is super soggy. If it seems very wet, pat it with a towel or squeeze a little, otherwise the moisture helps keep muffins tender.

Q: Can I replace the eggs or oil for a vegan version? A: You can swap eggs with flax or chia "eggs" 1 tbsp ground flax + 3 tbsp water per egg (so 2 tbsp flax + 6 tbsp water for this recipe). Oil can be replaced with melted coconut oil or extra applesauce but the texture may be slightly different.

Q: How do I know when they're done baking? A: Bake at 350 F for about 18 to 22 minutes. A toothpick in the center should come out with a few moist crumbs, not raw batter. Dont overbake or they'll dry out.

Q: Can I change the sweetener or chocolate? A: Yes. Maple syrup can be swapped for honey in equal amounts, or reduce to 1/4 cup if you want less sweet. Dark chocolate chips can be replaced with chopped chocolate, semi sweet chips, or omitted entirely.

Q: How should I store or freeze them? A: Store cooled muffins in an airtight container at room temp for 2 to 3 days or in the fridge up to a week. To freeze, cool completely, freeze on a tray then bag them for up to 3 months. Reheat in a 350 F oven for 8 to 10 minutes or microwave 25 to 60 seconds.

Healthy & Moist Chocolate Zucchini Muffins Recipe Substitutions and Variations

Whole wheat pastry flour or regular whole wheat flour: swap for all purpose flour (same amount) or a gluten free 1 to 1 flour blend (use same cups, crumb might be a bit different)
2 large eggs: use 2 flax eggs made from 2 tbsp ground flaxseed mixed with 6 tbsp water, let sit 5 minutes, or 1/2 cup silken tofu, blended, for similar moisture and binding
1/3 cup pure maple syrup: honey works in equal volume but will change the flavor and is not vegan, or 1/3 cup packed brown sugar for a less liquid option, add a tablespoon extra applesauce if batter seems dry
1/2 cup dark chocolate chips or chopped dark chocolate: swap for 1/2 cup chopped nuts like walnuts or pecans for crunch, or 1/2 cup cacao nibs if you want a more bitter chocolate punch

Pro Tips

1. Squeeze the zucchini but don’t make it bone dry, you want it moist so the muffins stay tender, not dripping or they’ll water down the batter and make the crumb gummy.

2. Toss the chocolate chips with a teaspoon of flour so they don’t all sink, and press a few on top of each muffin for better looking tops when they bake.

3. Measure the flour by spooning it into the cup then leveling it off, otherwise packing it will make the muffins dry, and don’t overmix once you add the wet stuff or they’ll get tough.

4. If you want a moister, fresher feel after a day or two, freeze extras flat in a zip bag and microwave for 12 to 18 seconds to revive them, or warm briefly in a toaster oven for a slightly crisp top.