Warmly spiced, perfectly moist, and packed with hidden veggies — these zucchini carrot muffins taste like carrot cake and pass the toddler test every single time.
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For more healthy zucchini muffin recipes, check out my Blueberry Zucchini Muffins, Chocolate Zucchini Muffins, and Banana Zucchini Muffins.
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My toddler will eat almost anything if it comes in muffin form — these zucchini carrot muffins included. There's something very satisfying about watching a three-year-old enthusiastically eat zucchini and carrots while asking for more. The hidden veggie win is real.
These healthy zucchini muffins taste just like carrot cake muffins — warmly spiced, perfectly sweet, and incredibly moist — with a crunchy turbinado sugar top that makes them look bakery-made. They're made with applesauce and Greek yogurt instead of a full pour of oil, which keeps them light without sacrificing any of that moist, tender crumb. Whether you call them carrot zucchini muffins or zucchini muffins for toddlers, they're the recipe I make on repeat whenever zucchini season hits and the garden starts getting out of hand.
For more ways to use up summer zucchini: Zucchini Cake, Gluten-Free Zucchini Bread, Cheesy Zucchini Casserole, and The 20 Best Zucchini Recipes.
How to Prep the Zucchini & Carrots
Getting this step right is what makes the difference between a perfectly moist muffin and a gummy one.
Do you need to squeeze zucchini for muffins? Yes — lightly squeeze shredded zucchini in a clean kitchen towel or paper towels before adding it to the batter. Zucchini has a high water content that can make muffins gummy if not drained. You don't need to squeeze aggressively — just a gentle press to remove the excess moisture is all it takes.
How to shred: A box grater with the large holes works perfectly for both zucchini and carrots. A food processor with a shredding attachment is faster for bigger batches.
How much do you need:
- 1 medium zucchini = about 1 to 1½ cups shredded
- 2–3 medium carrots = about 1 cup shredded
Do you peel the carrots? Yes — peeled carrots shred more finely and blend into the batter better. Pre-shredded store-bought carrots work in a pinch but tend to be drier and thicker. Freshly shredded gives the best texture and moisture.
Can you use frozen zucchini? I don't recommend it — frozen zucchini releases too much water even after squeezing, which can make the muffins gummy.
The Applesauce & Yogurt Combo
Wondering what makes these healthy zucchini muffins different from the rest? Using both applesauce and Greek yogurt:
- Applesauce — This replaces a portion of the oil, adding moisture and natural sweetness without extra fat. It keeps the muffins tender and light — otherwise, you'd never know it was there.
- Greek yogurt — Adds a small protein boost, contributes to a soft, tender crumb, and adds a subtle tang that balances the sweetness. Plain or vanilla both work.
The result: These muffins are incredibly moist without being greasy, and they hold up well at room temperature for days — which is exactly what you want for a make-ahead snack or breakfast.
Important Ingredients and Substitutions
Avocado oil — Neutral-flavored and a great source of healthy fats. Canola or grapeseed oil substitute 1:1.
Applesauce — Use unsweetened. Sweetened applesauce makes the muffins too sweet. Mashed ripe banana substitutes well for a slightly different flavor profile.
Greek yogurt — Vanilla or plain both work. Full-fat gives the richest texture. For dairy-free, use coconut yogurt.
Flour — All-purpose gives the lightest texture. Whole wheat pastry flour adds whole grains and a slightly nuttier flavor without making the muffins dense. Regular whole wheat flour can be used, but it will make a denser muffin.
Brown sugar — Packed light brown sugar adds moisture and a warm molasses note. Don't substitute all white sugar — the moisture content matters here.
Turbinado sugar — The crunchy topping that makes these muffins look and feel bakery-made. Sanding sugar or coarse raw sugar substitutes well.
Cinnamon & nutmeg — The warm spice base that makes these taste like carrot cake. Don't skip the nutmeg — even a small amount adds depth.
Recipe Variations
Mix these carrot zucchini muffins up with any of these swaps and add-ins:
- Chocolate Chip — Fold in ½ cup mini chocolate chips before scooping the batter. Kids lose their minds for these. Worth making.
- Walnut or Pecan Crunch — Fold ½ cup of chopped walnuts or pecans into the batter for a nutty crunch that leans into the carrot cake vibe.
- Raisin Version — Add ⅓ cup of red or golden raisins for a more classic carrot cake flavor. Cranberries work great, too.
- Mini Muffins — Use a mini muffin tin and reduce the bake time to 10–12 minutes. Perfect for toddler snacks and little hands.
- Gluten-Free — Use a 1:1 gluten-free flour blend. and add 1 extra tablespoon of Greek yogurt for moisture. Let the batter rest for 30 minutes before baking, and cool entirely before enjoying.
- Dairy-Free — Substitute coconut yogurt for the Greek yogurt. The rest of the recipe is already dairy-free.
- Cream Cheese Frosted — Skip the turbinado sugar topping, and frost cooled muffins with cream cheese frosting for a full carrot cake muffin experience.
How to Make Zucchini Carrot Muffins
For the complete recipe and measurements, scroll to the recipe card at the bottom of this post.
Prepare: Preheat the oven to 400°F and move the baking rack to the center. Line 2 cupcake pans with 12 liners, placing them in every other cup. Brush the top of the pan around each liner with oil or butter.
Step 1: In a large bowl, whisk together the oil, applesauce, yogurt, eggs, vanilla extract, brown sugar, and white sugar until combined.
Step 2: Place the shredded zucchini in a clean tea towel or paper towels and squeeze out the excess moisture.
Step 3: Add the shredded zucchini and carrots to the wet ingredients and stir until combined.
Step 4: In a separate bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, and nutmeg.
Step 5: Add the dry ingredients to the wet ingredients. Fold until just combined — do not overmix.
Step 6: Scoop the batter evenly into the prepared muffin cups, about ⅓ cup per cup. Sprinkle 1 teaspoon of turbinado sugar over each muffin.
Step 7: Bake at 400°F for 5 minutes. Rotate the pan 180 degrees and reduce the temperature to 350°F. Bake 15–20 minutes more until a toothpick inserted in the center comes out clean.
Cool the pans on a wire rack for 5–10 minutes, then transfer the muffins directly to the rack to cool completely.
Chelsea's Recipe Pro-Tips
- Use room temperature eggs — Cold eggs don't incorporate as smoothly into the batter. Set them out 20–30 minutes before baking or place them in a bowl of warm water for 5 minutes.
- Don't overmix — Once the dry ingredients go in, fold gently until just combined. Overmixing develops gluten and makes muffins tough and dense.
- Fill every other muffin cup — Spacing the liners out allows better air circulation around each muffin, which helps them rise taller and bake more evenly. You'll get a better dome and more consistent results across the whole batch.
- Brush the pan with oil or butter — This prevents the muffin tops from sticking to the pan when they puff up and spread slightly over the liner edges. It makes cleanup easier and keeps your muffin tops intact.
- Don't skip the turbinado sugar — That crunchy, sparkly top is not just decorative. It adds a satisfying crunch and makes these taste like they came from a bakery.
- The two-temperature bake is intentional — Starting at 400°F gives the muffins an initial burst of heat that helps them rise quickly and develop domed tops. Dropping to 350°F finishes them through without overbrowning.
High-Altitude Adaptations
Developed and tested in Fort Collins, CO, at approximately 5,000 feet — one of the few zucchini carrot muffin recipes with real high-altitude testing behind it.
At 5,000+ feet:
- Increase flour to 2¼ cups (280g) for more structure
- Decrease baking powder and baking soda to ½ teaspoon each to prevent over-rising
- Reduce white sugar to ¼ cup (keep the same amount of brown sugar) to avoid gummy centers
- After the initial 5-minute bake, reduce temperature to 365°F instead of 350°F
At sea level: Follow the recipe as written. No adjustments needed.
Storage Directions
- Storing: Allow the muffins to cool completely before transferring to an airtight container. Keep at room temperature for up to 3 days or refrigerate for up to 5 days.
- Freezing: Cool completely, then freeze in a freezer-safe container or bag for up to 3 months. Wrap individually for grab-and-go convenience — great for toddler snacks all week. Defrost at room temperature for 30–60 minutes or microwave from frozen for 30–45 seconds.
- Reheating: Warm at room temperature or thaw muffins in the microwave for 20–30 seconds for a fresh-from-the-oven feel.
- Make-Ahead Tip: Make a double batch and freeze half. These muffins reheat beautifully and are among the best things to keep in the freezer for busy mornings.
Serving Suggestions
These zucchini carrot muffins are a perfect grab-and-go breakfast or snack any time of day. Pair one with a Pineapple Green Smoothie for a quick, balanced breakfast that works just as well for toddlers as it does for runners with early morning long runs.
For a more substantial morning, serve alongside Scrambled Eggs with Cottage Cheese for a protein-forward start that keeps everyone full until lunch. For the grown-ups, pair with a Protein Coffee for extra staying power on busy mornings.
Zucchini Carrot Muffin FAQs
Yes — gently squeeze shredded zucchini in a clean kitchen towel or paper towels before adding to the batter. Zucchini has a high water content that can make muffins gummy if not drained. A firm press is all you need — you don't have to wring it completely dry.
Almost always caused by too much moisture from the zucchini. Always squeeze shredded zucchini before adding it to the batter, and make sure your oven is fully preheated before baking. Underbaking is another culprit — a toothpick should come out completely clean.
Yes — these are one of the best muffins for toddlers. They're made without nuts (unless you add them), sweetened with a modest amount of brown and white sugar, boast healthy fats, and are packed with vegetables. The soft texture is easy for little ones to eat. My toddler devours them.
Yes — these freeze beautifully for up to 3 months. Cool completely, wrap individually, and freeze in a bag or container. Thaw at room temperature or microwave from frozen for 30–45 seconds. Make a double batch and freeze half for easy weekday snacking.
Not recommended — frozen zucchini releases significantly more moisture than fresh, even after squeezing, which can make muffins gummy. Stick to fresh zucchini for the best results.
Insert a toothpick into the center of a muffin — it should come out completely clean with no wet batter. The tops should be golden brown and spring back lightly when pressed.
Yes — pour the batter into a greased 9x5-inch loaf pan and bake at 350°F for 50–60 minutes, or until a toothpick comes out clean. Check at 50 minutes. Or try my dedicated Zucchini Carrot Bread recipe, developed specifically as a loaf!
Yes — substitute additional oil for the applesauce 1:1. The muffins will be slightly richer and denser. The applesauce version is lighter and lower in fat, which is why the recipe uses both.
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Recipe Card
Zucchini Carrot Muffins (Healthy, Moist & Toddler-Approved!)
Ingredients
- ½ cup avocado oil or canola or grapeseed oil
- ½ cup unsweetened applesauce
- ¼ cup vanilla or plain Greek yogurt
- 2 large eggs brought to room temperature
- 2 teaspoons pure vanilla extract
- ⅔ cup packed light brown sugar
- ⅓ cup white sugar
- 1 ½ cup shredded zucchini
- 1 cup shredded carrots preferably freshly shredded
- 2 cup (250g) all-purpose flour or whole wheat pastry flour
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- ⅛ teaspoon fine sea salt
- ½ teaspoon ground cinnamon
- ⅛ teaspoon ground nutmeg
- 3 tablespoons turbinado cane sugar or sanding sugar
Instructions
- Preheat the oven to 400°F with the rack in the center. Line 2 muffin pans with 12 liners, placing them in every other cup. Brush the top of the pan around each liner with oil or butter.
- In a large bowl, whisk together the oil, applesauce, yogurt, eggs, vanilla extract, brown sugar, and white sugar until smooth.
- Squeeze shredded zucchini in a clean tea towel or paper towels to remove excess moisture.
- Add the zucchini and carrots to the wet ingredients and stir until combined.
- In a separate bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, and nutmeg.
- Add the dry ingredients to the wet ingredients. Fold until just combined — do not overmix.
- Divide batter evenly into the prepared muffin cups (about ⅓ cup each). Sprinkle 1 teaspoon turbinado sugar over each muffin.
- Bake at 400°F for 5 minutes. Rotate pan 180 degrees and reduce heat to 350°F. Bake 15–20 minutes more until a toothpick comes out clean.
- Cool in pan on a wire rack for 5–10 minutes, then transfer muffins to the rack to cool completely.
Notes
- Every other cup — Spacing the liners allows better air circulation, helping muffins rise taller and bake more evenly.
- Brush the pan — Brushing oil or butter around each liner prevents the muffin tops from sticking when they puff over the edges.
- Squeeze the zucchini — Remove excess moisture with a tea towel before adding. Too much moisture = gummy muffins.
- Room temperature eggs — Set eggs out 20–30 minutes before baking for a smoother batter.
- Every other cup — Spacing liners out helps muffins rise evenly and develop domed tops.
- Don't overmix — Fold in dry ingredients just until combined for a tender crumb.
- Gluten-free — Use a 1:1 GF flour blend and add 1 extra tablespoon of Greek yogurt. Let the batter rest at room temperature for 30 minutes before baking and cool entirely before enjoying.
- Dairy-free — Substitute coconut yogurt for the Greek yogurt.
- Freezing — Freeze cooled muffins for up to 3 months. Thaw at room temperature or microwave 30–45 seconds from frozen.
- High altitude (5,000+ ft): Increase flour to 2¼ cups (280g), decrease baking powder and baking soda to ½ teaspoon each, reduce white sugar to ¼ cup, and lower the second bake temperature to 365°F instead of 350°F.
My toddler LOVES these! He seriously ate half a batch in about a day every time I made them while recipe developing and photographing for this recipe. 🙂
These are fantastic! Suddenly I have a lot more friends dropping by looking hopeful. No guilt muffins! I added 2 tbs chia seeds and about a cup of chocolate chips.