Need a healthy muffin recipe for your baby, toddler, or kids? These whole wheat applesauce muffins are an easy, lower sugar option! Made with added veggies (carrots), oats, ground cinnamon and ginger, flaxseed, and maple syrup and applesauce instead of sugar, they’re packed with nutrients and fiber. Serve them for breakfast, snack, or on the side of chili or soup, and watch them disappear!

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Lizzie’s Notes
As we come out of winter hibernation and enter the busy spring season, I’m looking for ALL of the easy recipes to feed my kids! I figured it was about time for another healthy muffin recipe, one that was veggie-loaded (of course) and full of good-for-you ingredients.
These applesauce muffins, made with a base of whole wheat flour and oats, fit the bill perfectly. They’re easy to make (like REALLY easy), freezer-friendly, and one of those recipes you’ll bake again and again. Don’t just take my word for it. My daughters (4 and 2) couldn’t wait for seconds when I served them for breakfast.
Be sure to read through my ingredient suggestions and tips before getting started. And come back and rate the recipe once you make it! I can’t wait to hear from you.

Ingredients and Substitutions
- Unsweetened applesauce: The key to moist muffins! You can use store-bought or homemade. Different brands have different levels of sweetness depending on the apples used, but I recommend choosing unsweetened over sweetened to keep this a low sugar muffin recipe.
- Maple syrup: Substitute honey or light brown sugar if desired. If you don’t want any added sugar, you could try to substitute mashed banana for the syrup. The muffins will not be that sweet though (but maybe that’s what you want).
- Egg: I have not tried this recipe without an egg, so I do not know if it would work with an egg substitute.
- Avocado oil: Substitute extra virgin olive oil or melted refined coconut oil. Melted butter also works fine.
- Vanilla extract
- Shredded carrots: I recommend grating the carrots yourself when making applesauce muffins! Use a grater with small holes (fine grate) for best results, so that the tiny carrots just melt into the batter. You can use store-bought shredded carrots, but they will change the texture of the muffins and make them a little lumpier/difficult to chew.
- Whole wheat flour: If needed, you can sub all purpose flour.
- Rolled oats: These are also known as old fashioned oats. You could use quick oats if that’s all you have, but the muffins may be a little denser if you do that.
- Flaxseed meal: You may see this called ground or milled flaxseed, depending on the brand. I really like the Trader Joe’s flaxseed meal and Spectrum Essentials ground flaxseed.
- Ground cinnamon and ginger: Consider adding a pinch of nutmeg for more spiced flavor.
- Baking soda, salt
Instructions
The full recipe card for applesauce muffins is at the bottom of the post. Here’s a preview of the steps with photos to guide you.

Whisk applesauce, maple syrup, egg, avocado oil, vanilla, and shredded carrots in a large bowl.

In a separate bowl (or just on top of the wet ingredients), stir the dry ingredients with a fork to combine. Add them to the wet ingredients. Mix with a rubber spatula until just combined.

Spoon batter into a muffin tray lined with paper liners or pieces of parchment paper.

Bake until a toothpick inserted in the centers of the muffins comes out clean, about 20 to 24 minutes at 350 degrees F/175 degrees C.
Equipment
As mentioned, I prefer using a fine grate hand grater (with small holes) for the carrots, so that they are well-incorporated into the batter. You can make this recipe using paper liners (my preferred brand) in a regular muffin tin or a silicone muffin pan.
Storage and Freezing
Whole wheat applesauce muffins can be stored in an airtight container, away from direct sunlight, on the counter for up to 3 days. To prolong storage and to ensure they don’t get overly moist, keep the container in the refrigerator for up to 5 days.
To freeze, let the muffins cool completely. Transfer to an airtight container or freezer-safe bag, removing as much air as possible when sealing. If you want to prevent freezer burn, consider wrapping each muffin in plastic wrap or parchment paper before putting them into the container. This also prevents them from sticking to each other.
Store in the freezer for up to 3 months. Thaw in the refrigerator or on the counter, or reheat in the microwave (after removing plastic wrap) in 20-second intervals on high until warmed through.

Serving
These are delicious on their own or spread with butter, nut butter, or cream cheese. I love serving them as part of a breakfast or brunch spread, on the side of my Broccoli Cheese Egg Bake or Sheet Pan Veggie Omelet for protein. They also taste great as a roll or biscuit substitute with chili or soup, especially during the fall and winter. Try them with my Healthy Pumpkin Chicken Soup!
More Healthy Muffins
Love these applesauce carrot muffins?! Check out my other healthy baked goods while you’re here:
📖 Recipe

Applesauce Muffins with Oats and Carrots
Ingredients
- 1 cup unsweetened applesauce
- ¼ cup maple syrup
- ¼ cup avocado oil
- 1 egg
- 2 teaspoons vanilla extract
- 1 cup finely grated carrots - from 2 medium carrots
- 1 cup whole wheat flour - flip to metric measurements for weight
- ½ cup rolled oats
- ¼ cup flaxseed meal
- 1 teaspoon baking soda
- 1 teaspoon ground cinnamon
- ½ teaspoon ground ginger
- ½ teaspoon salt
Instructions
- Preheat the oven to 350℉/175℃. Line a muffin tray with paper liners. Alternatively, you can use silicone liners or a silicone pan.
- In a large bowl, whisk the applesauce, maple syrup, avocado oil, egg, vanilla extract, and carrots.
- In a separate bowl, stir together the whole wheat flour, oats, flaxseed meal, baking soda, cinnamon, ginger, and salt with a fork or whisk to combine. Add the dry ingredients to the bowl of wet ingredients. Mix with a rubber spatula until just combined.
- Spoon the batter into the prepared muffin pan, dividing it evenly among the cavities. Each cavity will be filled almost to the top.
- Bake for 20 to 24 minutes until a toothpick inserted in the center of the muffins in the middle of the pan comes out clean.
- Enjoy warm or let cool and store for later!
- Leave a rating or review by tapping the stars on this recipe card (above) or in the comments section (at the end of the post)!
Notes
- Store leftovers in an airtight container on the counter (away from sunlight) for up to 2 to 3 days. The muffins get even moister over time, so to prolong storage, you can keep the container in the refrigerator for up to 5 days.
- To freeze, let the muffins cool then wrap each one in plastic wrap or parchment paper. Transfer to a freezer-safe container or bag, sealing and removing as much air as possible. Freeze for up to 3 months. Thaw in the fridge or on the counter. To quickly thaw in the microwave, remove the plastic wrap or parchment, place on a microwave-safe plate, and warm in 20-second intervals on high.






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