Want healthy meals your kids will love?

Whole Wheat Applesauce Muffins


These Applesauce Muffins are sweet, moist, fluffy and full of flavor even with 100% whole wheat flour!

Check out our recipe for making your own homemade applesauce!

close up of a whole wheat applesauce muffin broken in half on a plate

How to Make Whole Wheat Applesauce Muffins

Of all the muffins we have tried, these applesauce muffins are a good one to experiment with if you want to try 100% whole wheat.   Whole wheat muffins have a tendency to be denser or heavier, because the gluten develops more slowly than it does with white flour. Whole wheat baked goods also taste a little grittier than the white flour, depending on the type of whole wheat flour you are using. White flour is popular in baked goods because it can create a light and airy product, rather than dense and heavy.  But there are other facts that can help develop gluten and help baked goods to rise, even when you use 100% whole wheat.

whole wheat applesauce muffins with walnuts on top on a red checkered napkin

How to substitute Whole Wheat Flour for White Flour in a recipe

I’ve always taught that you can start with a small amount of equally substituted flour until your family gets used to the taste and texture of whole wheat.   Starting with 50% white flour and 50% whole wheat flour can have less impact on the finished product and give you a muffin very similar to one that you baked with all white flour.  However, as you start to move on the scale to more whole wheat than white, you can actually use LESS whole wheat flour.  One cup of all-purpose flour can be substituted for 3/4 cup whole wheat flour.

Because you are dealing with the whole grain, whole wheat flour doesn’t absorb the liquid in your muffins the way white flour does.  White flour acts more like a sponge and sops up all that liquid. So, with whole wheat flour, adding additional liquid can help make the muffins not too dry.

While not necessary in muffins, if cooking whole wheat bread, we will incorporate a small amount of gluten to help our whole wheat bread rise.  This is easy to do with products like Vital Wheat gluten.

overhead view of whole wheat applesauce muffins on a plate with sliced apples

What types of whole wheat flour is good for muffins

It surprises me how many different types of flours there are on the market now.  In fact, some whole wheat flours are as soft and smooth as white flour, and my kids are less likely to complain that something might taste “grittier”.

There are different types of wheat kernels that create different textures and tastes of whole wheat.   Here are a few of them:

  • White whole wheat flour– One type of wheat kernel that can be milled is called hard white wheat.  This is still 100% whole wheat, but the color is lighter, and the flour a little sweeter.
  • Whole wheat pastry flour– Whole wheat pastry flour is made from soft white wheat kernels, and creates a lighter flour, with less protein, which is good for baking.
  • Whole wheat self rising flour– This flour (whether from a white or red kernel) incorporates baking powder sifted into it to assist with baking.
  • 100% whole wheat flour– This term simply means that 100% of the kernel is present in the flour. The germ and endosperm are completely milled to create the flour.
  • Whole grain whole wheat flour 100% of the kernel– Again, the full kernel is milled, generally using the hard red wheat kernel.
  • Whole wheat flour – While sometimes it means the full kernel is milled, only 95% of the kernel is required to label the flour “whole wheat flour”.


stack of delicious 100% whole wheat applesauce muffins for kids with a bite taken out of one of the muffins

Health Benefits Whole Wheat Flour

If it can be tricky to create whole wheat muffins, you might be asking why do it at all? Absolutely!  When using the entire grain for your flour, instead of milling off the healthiest portions in favor of texture, it is healthier.  The three components of a whole wheat kernel include:

  • The bran- the most important part (which is taken away during milling of white flour). This contains the B-vitamins, the fiber, and important antioxidants!
  • The germ- this contains the protein, and even healthy fats!
  • The endosperm- contains the carbohydrate, the majority of the calories, and important minerals.


So, if you are ready to start incorporating more whole wheat into your muffins, start with these Applesauce Muffins!  Your kids will love them!

Applesauce muffins with nuts and brown sugar on a plate with a slice of apple

For more whole wheat muffins, check out these recipes:

whole wheat applesauce muffins with walnuts on top on a red checkered napkin
Print Recipe Pin Recipe
4.1 from 60 votes

Applesauce Muffins

Substitute white flour for whole wheat in these applesauce muffins to increase the fiber and vitamins!

Prep Time20 minutes
Cook Time15 minutes
Total Time35 minutes
Course: Breakfast
Cuisine: American
Servings: 12 2-3
Calories: 203kcal




  • Preheat oven to 400° F.
  • Mix dry ingredients together in a bowl (flour through salt).
  • In a separate bowl, whisk together eggs, applesauce, and brown sugar.
  • Melt butter; add to wet ingredients and stir to combine.
  • Fold wet ingredients into dry ingredients just until moist.
  • In a separate, small bowl, mix together walnuts and brown sugar for the topping.
  • Divide batter equally among muffin cups, then sprinkle on topping, pressing down lightly so it sticks.
  • Bake for 13-15 minutes or until a toothpick inserted into the center of a muffin comes out clean.
  • Cool for 5-6 minutes before serving.


Calories: 203kcal | Carbohydrates: 29g | Protein: 4g | Fat: 9g | Saturated Fat: 4g | Cholesterol: 44mg | Sodium: 120mg | Fiber: 2g | Sugar: 16g
Keyword : Applesauce Muffins


And to make your own applesauce, check out this canning applesauce post! 

Natalie Monson

I'm a registered dietitian, mom of 4, avid lover of food and strong promoter of healthy habits. Here you will find lots of delicious recipes full of fruits and veggies, tips for getting your kids to eat better and become intuitive eaters and lots of resources for feeding your family.

Learn More about Natalie

Leave a Comment:
Did you make this recipe? Leave a review!

Your email address will not be published. Required fields are marked *

Recipe Rating


These look delicious, my kids and I will be making these this afternoon!
It’s so refreshing to see recipes with real ingredients. Love your site ????

This looks yummy!
My son is allergic to eggs. I have typically used 1/4-1/3 cup of applesauce to substitute 1 egg. In this case i will be using 1.5 c applesauce. Do you suggest adjusting the amount of spices used?
Thank you !

Hi! making these for the kids now! I noticed in the directions it says to mix the vanilla with the other wet i greditonets but there is no amount listed for vanilla. Just thought I’d let you know. I decided to use 1 teaspoon.

I tried this recipe and it turned out so good. Loved how subtle the sugar is and so happy to use whole wheat instead of all purpose flour. I didn’t have muffin tin so used my mini muffin tin and baked for ten minutes and they were perfect bite size for lunchbox

5 stars
I really was skeptical. How could these be good?? But they are excellent! Thank you. I substituted Truvia brown sugar to cut a few more calories. Thank you Amy!

Came upon this recipe while hunting for applesauce whole wheat muffins. I’m confused: what does 33/100 cup brown sugar mean?

Hi Mary, sorry for the confusion! We made some big updates to our site over the weekend and it caused some technical issues with our recipes. Everything should be patched up now and the recipe amounts should look normal again. Thanks for your patience!

5 stars
Just made these (as mini muffins) for my 1 year old. They’re so good! She and my husband are devouring them!
Cooked 10 mins at 375 as mini muffins.

5 stars
This is a great base recipe. I modified it by adding 1/4 c or so flax seeds, 1/2 c or so dried currants, 1/4 c or so toasted sunflower seeds (plus some on top ). I left out the walnuts (we love them ,but I was running low), substituted canola oil for the butter, and used homemade pear-cranberry sauce instead of applesauce. They turned out beautifully and the recipe was flexible enough to allow me to use what I had on hand. I will make these again!

5 stars
I have made these muffins a few times and I’m thinking of making them again today. They are so quick to make and a perfect healthy treat. They freeze great and I take them to work as a snack or on trips for the kids.

5 stars
I’ve been trying to cut the junk foods and sugars and snacking on junk out. And this was totally the best snack and breakfast on the go helper. I love that there isn’t a million cups of sugar. It was what I had in the pantry and so easy to make. Thank you.

5 stars
A simple but very delicious muffin! The kids and hubby loved them. I found them very fluffy and moist. I didn’t add any topping to avoid mess from the kids and I also used coconut oil instead of better to try and give it an extra nutritional boost. These will be on my weekly rotation for sure!

5 stars
These are SO good! I just made them (like 10 minutes ago). They aren’t too dense (make sure you don’t over-mix) and they are just sweet enough. Best of all, my house smells like fall. Great recipe.

5 stars
My husband loved these. Do they need to be refrigerated? How long can they stay on the counter if not? Will freeze some to have on hand. What else can replace the butter? Thanks

Glad they were a husband win! We usually let them sit on the counter for a day or two. Any longer than that and I would freeze them or put them in the fridge to keep them fresh! And you can replace the butter with a neutral oil.