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You’ll love these simple applesauce muffins because not only are they incredibly quick and easy, they’re deliciously moist, flavorful, and satisfying. Packed with wholesome ingredients like whole wheat flour, oats, and applesauce, these healthful muffins are naturally free from refined sugar and contain no dairy if using non dairy milk. There’s no mixer required and you can play around with the add-ins for varying flavors and textures. Enjoy!

healthy whole wheat applesauce muffins

When I’m looking to bake something quick, easy, and wholesome—I always rely on muffins. Banana muffins or these apple cinnamon oatmeal cups are my top choices because they’re simple, relatively healthy, and adult + child approved. Preparing muffin batter is a no-fuss task and you can enjoy muffins right away, which is definitely a bonus when baking for or with kids. (By the way, here are many kid-friendly baking recipes.)

These applesauce muffins join my top favorites and I know you’ll love them too!

Why You Will Love These Applesauce Muffins:

  • Recipe is quick & easy
  • Muffins are satisfying, soft, & moist
  • No mixer required
  • Use convenient, ordinary ingredients
  • Healthful & wholesome just like these healthy apple muffins
  • No refined sugar
  • Dairy free if using a dairy free milk
  • optional add-ins for texture and flavor (raisins, nuts, chopped apples)

By the way, if you’re looking for a more indulgent apple muffin, try these apple cinnamon muffins.

whole wheat applesauce muffins with oats on top

Recipe Testing Whole Wheat Applesauce Muffins

Well well well. What ended up as a fairly easy muffin recipe began as complicated mess of sticky flavorless muffins. I started testing this applesauce muffin recipe using the base of my blueberry oatmeal muffins. Adding applesauce did the batter no favors and the entire muffin tasted bland and gloppy (technical terms). I adore that recipe and now know that it’s best to leave it alone.

So I turned to my whole wheat banana walnut muffins as a starting point. The batter includes oats as an add-in, so it’s less of an oatmeal muffin and more of a standard muffin with some oats in it—if that makes sense. I swapped applesauce for the mashed banana, added more oats, and slightly reduced the baking soda. (1 full teaspoon is simply not needed.) As it turns out, I think I prefer these applesauce muffins because I don’t always have brown & spotty bananas on hand. Convenience is key!

Key Ingredients in These Whole Wheat Applesauce Muffins

  1. Applesauce: Use unsweetened applesauce. If all you have is sweetened, that’s completely fine, just be sure to slightly reduce the maple syrup in the recipe. See recipe note below.
  2. Melted Coconut Oil: Without some fat, these muffins taste dry and rubbery. I love using melted coconut oil like we do in these healthier chocolate banana muffins, but vegetable oil or melted butter works too.
  3. Maple Syrup: The applesauce muffins aren’t overly sweet because using too much sugar takes away from the applesauce flavor. Maple syrup replaces refined sugar and pairs wonderfully with the applesauce.
  4. Whole Wheat Flour: These are 100% whole wheat muffins made with all whole wheat flour. If needed, you can switch out with all-purpose or white whole wheat flour. I have not tested this recipe with any gluten free flour alternatives. If you have leftover whole wheat flour from making honey wheat English muffins, this is the perfect place to use it!
  5. Oats: Use whole oats or quick oats in this recipe and there’s no need to soak them prior to using in the batter like we do with blueberry oatmeal muffins.
  6. Add-Ins: Like zucchini muffins, today’s thick muffin batter welcomes add-ins such as raisins, chocolate chips, dried cranberries, or chopped nuts. Based on sweetness of the add-in, it’s best to use either 3/4 or 1 cup as detailed in the notes below. You could also use 1 and 1/2 cups of chopped apples (about 2 medium). We love them with raisins because they remind us of bran raisin muffins which are made with wheat bran—an ingredient I don’t usually have on hand.

You also need cinnamon, baking powder & baking soda, salt, eggs, milk, and vanilla extract. Before baking, you can sprinkle the tops of the muffins with oats and/or coconut sugar or coarse sugar for a little crunch. I like adding it to pumpkin muffins, too.

(Note in the photo below the melted coconut oil looks like ice water since not all of the oil had been melted– I melted it more after taking this photo.)

applesauce and other muffin ingredients shown in bowls

Best Applesauce To Use

The best applesauce to use for baking is typically unsweetened. In this recipe, you can use homemade or store-bought and the consistency doesn’t make a difference—thick, thin, smooth, or chunky. Applesauce with cinnamon is also a great choice, but if you don’t want too much cinnamon flavor, I would slightly reduce the cinnamon in the recipe.

My best advice is to use whatever applesauce you enjoy eating!

Imperative Success Tip: Make sure you grease the muffin liners before adding the batter or skip the liners and grease the muffin pan. This batter sticks to the liners, but greasing helps. After the muffins cool completely, they do not stick as much.

applesauce muffin batter in glass bowl and in muffin pan
whole wheat applesauce muffins in muffin pan
whole wheat applesauce muffins with raisins

The muffins above look like they have chocolate chips, don’t they? Chocolate chip lovers will be disappointed to learn those are raisins. HA! (Oh-so-good with raisins!)

Can I Add Apples?

Yes, apples are a wonderful choice as the add-in. See recipe note below.

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whole wheat applesauce muffins with oats on top

Applesauce Muffins

  • Author: Sally
  • Prep Time: 15 minutes
  • Cook Time: 21 minutes
  • Total Time: 40 minutes
  • Yield: 12 muffins 1x
  • Category: Muffins
  • Method: Baking
  • Cuisine: American


These moist and flavorful whole wheat applesauce muffins come together with a handful of healthful and wholesome ingredients. See notes if you wish to replace the raisins.


  • 2 cups (255gwhole wheat flour (spoon & leveled)
  • 2/3 cup (58g) old-fashioned whole rolled oats
  • 1 teaspoon ground cinnamon
  • 3/4 teaspoon baking soda
  • 1 teaspoon baking powder
  • 1/2 teaspoon salt
  • 1 and 1/3 cups (320g) unsweetened applesauce, at room temperature*
  • 2 large eggs, at room temperature
  • 1/3 cup (80ml) melted coconut oil (or use vegetable oil or melted butter)
  • 1/3 cup (80ml) pure maple syrup, at room temperature
  • 1/3 cup (80ml) milk (dairy or non dairy), at room temperature
  • 1 teaspoon pure vanilla extract
  • 3/4 cup (110g) raisins*
  • optional: 3 Tablespoons oats and/or 1 Tablespoon coarse sugar for sprinkling


  1. Preheat oven to 425°F (218°C). Spray a 12-count muffin pan with nonstick spray or use cupcake liners. If using cupcake liners, spray the liners because when warm, these muffins stick.
  2. Whisk the flour, oats, cinnamon, baking soda, baking powder, and salt together in a large bowl until combined. Set aside. In a medium bowl, whisk the applesauce, eggs, oil, maple syrup, milk, and vanilla together until combined. Pour the wet ingredients into the dry ingredients, stir a few times, then add the raisins. Fold everything together gently just until combined and no flour pockets remain.
  3. Spoon the batter into liners, filling them all the way to the top. Top with oats and a light sprinkle of coarse sugar, if desired. Bake for 5 minutes at 425 then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C). Bake for an additional 15-16 minutes or until a toothpick inserted in the center comes out clean. The total time these muffins take in the oven is about 20-21 minutes, give or take. (For mini muffins, bake 11-13 minutes at 350°F (177°C) the whole time.)
  4. Allow the muffins to cool for 5 minutes in the muffin pan, and then transfer to a wire rack to continue cooling or enjoy warm.
  5. Muffins stay fresh covered at room temperature for a few days, then transfer to the refrigerator for up to 1 week.


  1. Make Ahead Instructions: For longer storage, freeze muffins for up to 3 months. Allow to thaw overnight in the refrigerator, then bring to room temperature or warm up in the microwave if desired.
  2. Oats: This recipe uses whole rolled oats, but you can use the same amount of quick oats if needed. You can also skip the oats if desired, but I recommend adding a little more flour to help soak up some liquid, such as 3 Tablespoons (about 24g).
  3. Applesauce: It’s best to use unsweetened applesauce. If using sweetened, slightly reduce the maple syrup down to 1/4 cup (60ml). You can use homemade or store-bought applesauce and the consistency doesn’t make a difference– use thick, thin, smooth, or chunky. Applesauce with cinnamon is also a great choice, but if you don’t want too much cinnamon flavor, I would slightly reduce the cinnamon in the recipe.
  4. Maple Syrup: You can use honey for the maple syrup, but the flavor will be different.
  5. Raisins/Add-Ins: Feel free to leave the muffins plain, but they’re excellent with add-ins such as raisins, 3/4 cup (about 110g) dried cranberries, 1 cup (about 120g) chopped walnuts or pecans, 1 and 1/2 cups (165g) peeled & chopped apples (about 2 medium apples such as Granny Smith, Honeycrisp, Gala, Pink Lady), or 3/4 cup (about 135g) chocolate chips.
  6. Initial High Temperature: The hot burst of air will spring up the top of the muffin quickly, then the inside of the muffin can bake for the remainder of the time. This helps the muffins rise nice and tall.
  7. Room Temperature Ingredients: It’s best if any cold ingredients are brought to room temperature before starting. The coconut oil will slightly solidify if other ingredients are too cold and you may notice greasy oily pockets in the baked muffins.
  8. Nutrition Information: Using VeryWellFit calculator and calculated using coconut oil, unsweetened almond milk, and raisins, these muffins come out to 181 calories, 7.2g fat, 27g carbs, 3.3g fiber, 9g sugar, and 4g protein each.

Keywords: applesauce muffins

Reader Questions and Reviews

  1. Hi, I am looking forward to trying this recipe. I was thinking about making it in a 9 by 5 loaf pan instead of doing muffins, is there any reason why that wouldn’t work? Thanks!

    1. Hi Rachel, You definitely can! Any muffin recipe yielding around 12 standard size muffins can double as a quick bread recipe. We are unsure of the best bake time, but use a toothpick to check for doneness.

  2. I have always been a hit and miss baker. Now I read all your tips AND get your daily recipes. These muffins were awesome…..and now I can be a baker! Thanks Sally!

    1. Can I add regular flour and regular oats? I can’t have whole wheat.
      I don’t know how to add my own comment that’s why I am adding to another comment.

      1. Hi Emily, yes, you can use regular all purpose flour instead — same amount. This recipe uses whole rolled oats, but you can use the same amount of quick oats if needed. You can also skip the oats if desired, but we recommend adding a little more flour to help soak up some liquid, such as 3 Tablespoons (about 24g).

    1. Hi Shiloh, you can use honey instead of the maple syrup. Regular granulated or brown sugar would work as a substitution for maple syrup. (There is enough liquid in the batter).

  3. This is one of the BEST muffin recipes I have ever made. Consistently moist and delicious. I added a half cup of dried tart cherries and they are simply outstanding. I make them about every two weeks as they disappear pretty quickly. Thanks for this wonderful, healthy and easy recipe.

  4. Hello, I was looking for a bran muffin recipe and this one popped up. Would you say this is comparable to a bran muffin? Or would you recommend a different recipe? Thanks so much in advance!

    1. Hi Alejandra, We wouldn’t call this a bran muffin. Here are all of our muffin recipes if you want to take a look!

  5. These muffins are amazing! I reduced the maple syrup to 1/4 cup since I like my muffins on the less sweet side and they turned out great. The applesauce and raisins not only add flavor, moisture, and texture but also sweeten the muffin. The second time I made these muffins I was out of raisins, so I decided to add about two cups of blueberries instead and, well, that was a really great decision. Overall, these muffins are fluffy, wholesome, moist, and delicious!

  6. How can I make this recipe without oats? Would simply omitting them change the consistency or flavor? Thanks!

    1. Hi Lisa, You can skip the oats if desired, but we recommend adding a little more flour to help soak up some liquid, such as 3 Tablespoons (about 24g).

  7. All of the recipes I’ve made from your website have been winners, and this one is no different!! I added all the suggested mix-ins besides chocolate chips. They are wholesome and amazing. I loved the coarse sugar and oat topping. Your recipes are my favorite baking recipes on the whole internet!

  8. I was looking for Raising Bran muffins as I have already started printing all your others and have signed up for your email delivery.

    1. Hi Paula, we don’t have a bran muffin recipe at this time but we do love them! Let us know if you find a recipe you love 🙂

  9. Made these last night, just had to use different oil bc of coconut allergy. Made them in the giant muffin tins (had to bake wee bit longer)… They turned out AMAZING. All your recipes do! Thank you again

  10. While being healthy these muffins are not sweet enough. My main pet peeve is that sweets are too sweet! However I cannot taste the applesauce distinctly and they are very Bland

  11. These muffins are amazing! I added frozen blueberries and honey they were perfectly sweet and moist. We will be adding these to our morning muffin rotation. Thanks again, Sally!

  12. These muffins are delicious and perfect for breakfast. Thanks very much 🙂

  13. Hi Sally, I really love your recipes but I’m having a hard time understanding how much 1 cup of whole wheat flour is in grams. Maybe I’m just bad at math but several of your recipes that call for whole wheat flour uses different grams. Do you have a set number of grams for whole wheat flour like you do for all purpose and cake flour? Thx in advance.

    1. Hi Vanessa, 1 cup of spoon and leveled whole wheat flour is about 125-130g. And we usually get about 118g for 1 cup of spoon and leveled cake flour.

  14. These were very tasty. I made half the recipe and did a 60/40 whole wheat to white flour mix, used canola oil and a mix of white and brown sugar. I’ll definitely make them again, but maybe add some walnuts next time just to add protein.

    1. I’ve now made these 4 times in the last two weeks! My husband loves them too. They aren’t too sweet, have great texture and are pretty quick to make if planning ahead — making sure ingredients are room temperature. I actually have been using 70% whole wheat flour and 30% white and depending on who makes the applesauce in this house (my husband adds too much sugar), I may not put any sweetener at all in the muffins. But then I have been adding more raisins than the recipe calls for.

  15. I really like these muffins and make this recipe often. I substitute avocado oil for the coconut oil. I have heard that it is healthier and it is flavorless which I prefer. Also by using the avocado oil I don’t have to worry about my other ingredients being room temperature. I just throw in all of the ingredients straight from the refrigerator and I have never had a problem with the recipe.

  16. These are so good! Not too sweet. I made ours with 2 flax eggs rather than real eggs and they turned out great. Oh, also added a little handful of hemp hearts. Thanks for yet another great recipe!

  17. Do you think I could substitute some or all of the applesauce for Greek yoghurt?

  18. These applesauce muffins are one of my favorite muffin recipes out there. Comes together in minutes and is pretty easily adaptable. Since I rarely ever have maple syrup in the house, I subbed about 40g of brown sugar which was plenty sweet enough. I’ve also made them with monkfruit sweetener with success. Plus, the whole wheat flour and oats make these a welcome addition to my breakfasts. They’re wonderful plain, though perhaps next time I’ll add some apples or nuts. I love that they are freezer friendly as well. Thanks for another winner, Sally!

    1. Hi Patty, we don’t recommend it. Almond flour has very different baking properties than whole wheat flour and is not always a 1:1 swap. It would take a bit of recipe testing to determine the right amount. You might enjoy these blueberry almond muffins instead.

  19. These are delicious! I subbed half of the apple sauce with pumpkin puree and upped the spices with added ginger. I only had plain white flour so replaced half a cup of flour with ground linseed. Such a great recipe, and so versatile!

  20. I did a 1/2 white and 1/2 wheat flour mix. Then topped them with a cinnamon oat streusel crumble before baking. Very nice.

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