Bake moist, healthy zucchini muffins with whole wheat flour, honey, and dark chocolate chips - a wholesome treat for any time of day.
Even as a retired dietitian, I'm often asked if muffins can really be part of a healthy lifestyle.
My answer? Absolutely.
The key is balance and a few simple tweaks. By reducing the added sugar, swapping in nutrient-dense flours, and adding fiber-rich ingredients like zucchini, you can turn a classic muffin into something both delicious and better for you.
I always encourage starting small - make one change at a time so you can appreciate the natural flavors that shine through. Before long, you'll notice you don't miss the extra sugar or fat. In fact, the muffins taste even better when their ingredients are allowed to shine.
With this recipe, you'll see how easy it is to bake a batch of muffins that feel like a treat while still supporting a healthy lifestyle for you and your family.
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Prep and Bake Time
- Prep time: 10 minutes
- Bake time: 26 minutes
- Total time: 36 minutes
Ingredients
- All-purpose flour: for light and tender muffins
- Whole wheat flour: adds fiber and a hearty, wholesome texture
- Baking powder and baking soda: help the muffins rise and stay fluffy
- Ground cinnamon and ginger: warm spices that complement the zucchini
- Salt: just a pinch to balance the sweetness
- Egg: at room temperature for better mixing and structure
- Buttermilk: keeps the muffins extra moist and tender
- Honey: a natural sweetener instead of refined sugar
- Neutral oil: adds richness without overpowering flavor
- Fresh lemon juice and zest: brighten the muffins with a hint of citrus
- Zucchini: freshly grated for moisture and nutrition
- Dark chocolate chips: mini or regular, for a touch of indulgence
Step‑by‑Step: How to Make Zucchini Muffins
Preheat the oven. Set your oven to 425°F (220°C) and place the oven rack to the middle position. Line a muffin tin with 18 paper liners (you'll need one and a half pans).
Mix the dry ingredients. In a large bowl, whisk together:
- 1¼ cups (175 g) all-purpose flour
- 1- 1¼ cups (155 g to 194 g) whole wheat flour [SEE RECIPE NOTE]
- 2 teaspoons (8 g) baking powder
- ½ teaspoon (3 g) baking soda
- 1½ teaspoons (4 g) ground cinnamon
- ½ teaspoon (1 g) ground ginger
- and just a pinch of salt (about 1 g)
RECIPE NOTE: Zucchini can vary in water content depending on the season, size, and how finely it's grated. If your batter looks too thin, add a little more flour. For best results, you may need anywhere from 155 g to 194 g (1-1¼ cups) of whole wheat flour. Start with the lower amount and adjust as needed - the batter should be thick but scoopable.
Whisk the wet ingredients. In another bowl, whisk until smooth:
- 1 large egg, at room temperature
- 1 cup (240 mL) buttermilk at room temperature
- ⅔ cup (160 mL) honey
- ¼ cup (60 mL) neutral oil
- 2 tablespoons (30 mL) freshly squeezed lemon juice
- and the zest of half a lemon.
- Add the zucchini. Stir in 1-1¼ cups (about 130-150 g) of grated zucchini into the liquid ingredients and mix thoroughly with a wooden spoon or rubber spatula.
- Combine wet and dry. Pour the wet mixture (with zucchini) into the dry ingredients. Gently stir with a wooden spoon or spatula until the flour just disappears. Don't overmix - a few streaks are fine.
- Fold in the extras. Stir in ½ cup (90 g) dark chocolate chips (mini or regular).
- Fill the muffin cups. Divide the batter evenly among the 18 liners, filling each about three-quarters full.
- Bake tall, bake golden. Bake at 425°F (220°C) for 5 minutes, then (without opening the oven door) reduce the temperature to 375°F (190°C) and bake for another 21-25 minutes, or until the top bounces back when lightly touched.
Cool and enjoy. Let the muffins rest in the pan for 5 minutes before transferring them to a wire rack to finish cooling.
Tips
- Start hot: Bake at 425°F (220°C) for 5 minutes, then lower to 375°F (190°C) to get tall, domed muffins without drying them out.
- Measure flour correctly: Spoon and level your flour, or use a kitchen scale, to avoid dense muffins.
- Don't peel the zucchini: The skin is tender and adds pretty green flecks. Just wash and grate.
- Squeeze lightly: If your zucchini is very watery, give it a gentle squeeze - but don't dry it out completely.
- Use room temperature ingredients: Egg and buttermilk blend more smoothly when not cold, creating a tender crumb.
- Mix-ins: Not into chocolate? Swap the chips for nuts, raisins, or blueberries.
- Cool quickly: Let muffins rest in the tin for just 1-2 minutes, then transfer to a wire rack. This prevents soggy bottoms from trapped steam.
FAQ
No, the zucchini adds moisture and tenderness, but the flavor blends right in with the chocolate and spices.
Nope! The skin is thin and tender. Just wash, trim the ends, and grate. The green flecks actually look pretty in the muffins.
It depends on how moist your zucchini is. If your zucchini is very watery, give it a light squeeze. You still want some moisture left - it helps keep the muffins soft and moist.
Zucchini can hold very different amounts of water depending on the season, size, and how finely it's grated. That extra moisture affects the batter. For this recipe, you may need anywhere from 155 g to 194 g (1- 1¼ cups) of whole wheat flour. Start with the lower amount and add more if the batter seems too thin - it should be thick but scoopable before baking.
It depends on your preference. I like zucchini that's coarsely grated because it adds a little texture and those pretty green flecks in the muffins. If you'd rather the zucchini blend in completely, grate it more finely. Both methods work - the texture is the only difference.
Yes. Replace the buttermilk with any plant‑based milk.
No problem! Just use all-purpose flour for the full amount. The muffins will be a little lighter in texture but still delicious.
Once completely cooled, keep the muffins in an airtight container at room temperature for up to 2 days. For longer freshness, store them in the fridge for up to 5 days.
Yes! These muffins freeze beautifully. To preserve the freshness and prevent freezer burn, wrap each muffin individually in plastic wrap before placing them in a tightly sealed freezer bag or container. When ready to eat, allow the muffins to thaw overnight at room temperature, then reheat them in an oven.
More Muffin Recipes
Recipe Inspiration
This recipe for zucchini muffins goes back over a decade ago for me. I first came across a version from the Dairy Farmers of Canada, and over time I gave it my own twist - adjusting the spices to suit my taste, swapping part of the flour for whole wheat, and replacing the milk with buttermilk for extra tenderness.
You will notice that I prefer zucchini that's coarsely grated - it gives the muffins a little texture and those pretty green flecks. If you'd rather the zucchini "disappear" into the batter, you can grate it more finely. Both work - it just depends on your texture preference.
The result is a muffin that's moist, lightly sweet, and filled with wholesome ingredients.
In fact, every summer when zucchini is in season, this recipe makes a regular appearance in my kitchen - and I hope these muffins find a place in your kitchen, just as they have in mine.
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Maria
★★★★★ If you have made this recipe for zucchini chocolate chip muffins, I would love to hear about it in the comments below and be sure to rate the recipe!
Recipe
How to Make Healthy Zucchini Muffins
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Ingredients
- 1¼ cup all-purpose flour 175 grams
- 1- 1¼ cup whole wheat flour 155-194 grams
- 2 teaspoons baking powder 8 grams
- ½ teaspoon baking soda 3 grams
- 1½ teaspoons cinnamon ground, 4 grams
- ½ teaspoon ginger ground, 1 gram
- pinch salt 1 gram
- 1 egg room temperature
- 1 cup buttermilk room temperature, 240 mL
- ⅔ cup honey liquid, 160 mL
- ¼ cup vegetable oil 60 mL
- 2 tablespoons lemon juice freshly squeezed, 30 mL
- zest of half a lemon
- 1-1¼ cup zucchini grated, about one small zucchini, 130-150 grams
- ½ cup chocolate chips dark, mini or regular, 90 grams
Instructions
- Set your oven to 425°F (220°C) and position the rack in the middle. Line a muffin tin with 18 paper liners.
- In a large mixing bowl, whisk together both flours, baking powder, baking soda, and spices. Set aside for now. SEE RECIPE NOTE
- In a separate bowl, whisk together egg, buttermilk, honey, oil, lemon juice and zest.
- Stir in the grated zucchini with the wet ingredients and combine.
- Pour the wet mixture (with zucchini) into the dry ingredients. Gently stir with a wooden spoon or spatula until the flour just disappears. Don't overmix - a few streaks are fine.
- Gently fold in the dark chocolate chips until just combined.
- Fill muffin liners ¾ full.
- Place the muffins in the oven at 425°F (220°C) for 5 minutes. Without opening the door, reduce the temperature to 375°F (190°C) and continue to bake for 21-25 minutes or until the top bounces back when lightly touched.
Video
Notes
Nutrition
This post was originally published on July 24, 2016, and republished on August 21, 2021, and again on September 5, 2025, with updated content and photos. Thanks for sharing!
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Margaret
I made these zucchini muffins the other day. They were fantastic! I used a generous 1 1/4 cup shredded zucchini but I squeezed out the excess water before adding it to the batter since I was using an overgrown zucchini from my garden. I only had 2/3 cup whole wheat flour so I made up the rest with spelt flour. I divided the entire batter into 12 muffin tins instead of 18 and baked for about 25 minutes. What I liked about this recipe was that the finished muffins rose beautifully and weren’t too sweet or oily. I’ll definitely be making these again.
Maria
So thrilled to read this! Thanks so much for sharing Margaret!