Healthy Apple Crisp Muffins

Loaded with apples, warm spices and crunchy oat topping, these Healthy Apple Crisp Muffins will be your new favorite fall breakfast! These muffins taste similar to apple crisp, but without all the extra sugar and butter. So you can definitely enjoy more than one!

Fall is just around the corner with its colorful leaves, cozy sweaters and pumpkin spice everything. Now, don’t get me wrong, I love pumpkin spice flavor, especially when it comes to muffins, ice cream or cake. Sometimes, however, grocery stores go a bit too far with this popular flavor. In the midst of all the pumpkins, I need a little break, which is why I created these apple crisp muffins. Move aside, pumpkins, and make way for apples!

Every year, my family and I go out to my great-grandpa’s farm and pick buckets and buckets of apples and pears. And, every year, my mom and I have to figure out how to use the huge buckets of fruit we have collected! Because the apples we get at our family farm are not genetically modified like grocery store apples, they are sour and not very sweet. They are not pleasant to eat on their own, which is why I often make several batches of these apple crisp muffins.

When choosing apples for your muffins, I would recommend using a sweeter apple. I obviously use really sour ones, but, in the past, I have made these muffins with sweeter apples and they are better. But, whatever you have on hand will work. Just keep in mind that the sweeter your apples are, the sweeter your muffins will be.


The ingredients in these muffins are super simple and can be found at any time of year at your local grocery store. And here’s another plus: a full four cups of fruit are packed into this recipe!

Whole Wheat Flour~ With fiber and nutrients, this flour is a healthier choice for muffins and quick breads. I love that it adds a boost of whole grains to your breakfast, without creating a dense or gummy texture!

Brown Sugar~ For this recipe, I like to use brown sugar because it deepens the apple spice flavors. If you don’t have brown sugar, you can use white sugar. I have not tried substituting honey, maple syrup or agave, but feel free to experiment.

Salt, Baking Powder and Baking Soda~ Salt is important because it elevates the sweetness and flavor of the muffins. Baking powder and baking soda are essential to making sure that the muffins rise evenly and are fluffy.

Cinnamon, Clove, Nutmeg and Ginger~ These spices are the key to making delicious apple crisp muffins! Yes, one tablespoon of ground cinnamon seems like a lot, but I promise that the taste of these muffins is absolutely amazing. The ground cloves, nutmeg and ginger also add tremendous apple spice flavor.

Eggs~ Two eggs help bind all of the ingredients together and assist in leavening the muffins. If you wish, you may substitute two flax eggs (3 tbsp ground flax mixed with 1 tbsp water makes one egg) or an extra 1/2 cup of applesauce for the eggs. Just be warned that the texture will be gummy.

Unsweetened Applesauce~ Applesauce is wonderful for making soft, moist muffins, without adding excess oil! I love that this recipe packs two full cups of applesauce, plus all of those chopped apples into just 18 muffins! You could substitute mashed banana if you don’t have applesauce. And, if you can’t find unsweetened applesauce, sweetened will work too.

Chopped Apples~ Any variety of apple will work in this recipe. Granny Smith, Gala or Pink Lady are some of my favorites for baking. The sweetness of your apples will determine how sweet your muffins are. I peeled my apples before chopping them into small pieces, but if you don’t mind apple peel, don’t worry about that step. You can’t really tell the peel is in the muffins at all.

Crisp Topping Ingredients

Rolled Oats~ I like to use old-fashioned rolled oats, but you can use quick oats in a pinch. Do not use steel-cut oats because they will be tough and hard to chew.

Chopped Walnuts~ I used walnuts, but you can use pecans or even almonds. If you don’t like nuts or have an allergy, you can simply substitute another 1/4 cup of rolled oats for the nuts.

Brown Sugar and Cinnamon~ These two ingredients add flavor to the crisp topping, making it deliciously addictive!

Oil~ I used canola oil, but you can use vegetable, olive or melted coconut oil, or even melted butter.

The Dance

I love the simplicity of muffins! The only part to this recipe that takes a little extra time is chopping the apples. You want to make sure the apple pieces are small, but not so small that you can’t tell that the apples are there.

After chopping the apples, whisk together the dry ingredients.

Add the wet ingredients to the dry and then fold in the apples.

For the crumble topping, stir together the crumble ingredients in a small bowl. Portion the batter in between 18 muffin molds and sprinkle with the topping.

Bake until the topping is golden brown and a toothpick inserted into a muffin comes out clean. I would allow these to cool completely before enjoying because the texture and flavor is better.

For best results, wrap yourself in a cozy blanket and enjoy your muffin with a hot cup of tea. 🙂

Healthy Apple Crisp Muffins

Loaded with apples, warm spices and crunchy oat topping, these Healthy Apple Crisp Muffins will be your new favorite fall breakfast! These muffins taste similar to apple crisp, but without all the extra sugar and butter. So you can definitely enjoy more than one!
5 from 6 votes
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Course Breakfast
Cuisine American
Servings 18 muffins
Calories 130 kcal


  • 12 count muffin pan


Muffin Ingredients

  • 2 cups whole wheat flour
  • 1/2 cup brown sugar
  • 1 tsp salt
  • 1 tsp baking powder
  • 1/2 tsp baking soda
  • 1 tbsp ground cinnamon
  • 1/2 tsp ground cloves
  • 1/2 tsp ground nutmeg
  • 1/2 tsp ground ginger
  • 2 large eggs
  • 2 cups unsweetened applesauce
  • 2 cups chopped apples

Crisp Topping Ingredients

  • 1/4 cup old-fashioned oats
  • 1/4 cup chopped walnuts or pecans
  • 2 tbsp brown sugar
  • 1 tsp ground cinnamon
  • 1 tbsp canola or vegetable oil


  • Preheat your oven to 350 degrees fahrenheit and grease 18 muffin molds with cooking spray or line with cupcake liners.
  • In a large bowl, whisk together the flour, brown sugar, salt, baking powder, baking soda, cinnamon, cloves, nutmeg and ginger.
  • To the dry ingredients, add the eggs and applesauce. Stir until just combined before folding in the chopped apples. Set the bowl aside.
  • For the crisp topping, in a small bowl, stir together the oats, nuts, brown sugar, cinnamon and oil.
  • Divide the muffin batter between the prepared muffin cups and sprinkle with the topping. Bake for 18-20 minutes or until a toothpick inserted into a muffin comes out clean. Allow to cool before serving.


*If you have another muffin tin, grease that one too because this recipe makes 18 muffins. However, if you only have one pan, simply bake the batter in batches.
*Store leftover muffins in an airtight container in the fridge for up to 3 days. After 3 days, place muffins in the freezer and freeze for up to 3 months. Thaw in the microwave or overnight in the fridge before eating.
Keyword apples, easy, healthy, muffins

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