Healthy breakfast ideas are always something I’m looking for! These healthy apple cinnamon breakfast cookies are a family favorite and so perfect for grabbing as you walk out the door.

They are high in fiber, low in fat and sugar and full of flavor! And who doesn’t want cookies for breakfast?!

a photo of two healthy breakfast cookies stacked on each other full of raisins and pepitas

I’ve had this breakfast cookie recipe in a photocopied hand-out for years. When my husband & I started riding the bus at 6:15 every morning, I started looking for fast and healthy breakfast recipes. I pulled this one out, made some changes to lower the fat and raise the fiber and this is what I got. In addition to a healthier recipe, the cookies turned out to be more moist and tastier than ever!

I feel like there are a few breakfasts that I love, but I know aren’t good for me (hello french toast and killer breakfast sandwiches!) and they wont keep me satisfied in a healthy way which means I’ll be making poor decisions all day. I try to choose better breakfast choices all week, like these breakfast cookies and then save pancakes for Saturday morning. One day a week doesn’t kill ya, especially if you’re still smart about what you eat for your other meals.

What Do I Need to Make Healthy Breakfast Cookies?

These cookies are packed with healthy ingredients and loads of flavor. Here is what you will need:

  • Whole Wheat Flour
  • Oat Flour
  • Baking Powder
  • Salt
  • Cinnamon
  • Cardamom
  • Apple Butter
  • Brown Sugar
  • Egg
  • Vanilla
  • Apple
  • Oatmeal
  • Pepitas
  • Raisins

The measurements for each ingredients can be found in the recipe card below.

a photo of two healthy breakfast cookies stacked on each other full of raisins and pepitas

How to Make Healthy Breakfast Cookies

These breakfast cookies come together quickly, and if you limit yourself to two a day (so hard!), then you’ve got breakfast for the whole week! Here are the basic steps:

  1. Preheat the oven.
  2. Combine all the dry ingredients.
  3. Add all the wet ingredients.
  4. Fold in all the chunky ingredients.
  5. Spoon the dough onto a greased cookie sheet and smash them down a little.
  6. Bake and cool.
More detailed ingredients can be found in the recipe card at the end of the post.

Is Whole Wheat Flour Better Than All Purpose?

Whole wheat flour is rich in vitamins B-1, B-3, and B-5, and contains riboflavin and folate.

Whole wheat flour also has more iron, calcium, protein, and other nutrients than white flour.

Is Apple Butter the Same as Applesauce?

Applesauce is lighter and has more water content than apple butter.

Apple butter has a more buttery or jam-like consistency.

Apple butter is a spread, it is closer to a jam than a sauce.

a photo of two healthy breakfast cookies stacked on each other full of raisins and pepitas

Can You Substitute Applesauce for Apple Butter in Recipes?

Applesauce will usually work as a substitute, but you may need to make an adjustment or two.

Apple butter is sweeter and more concentrated than applesauce, so you may need to add a little brown sugar to the recipe.

Can Breakfast Cookies Be Frozen?

These cookies are freeze great. I like to make a double or triple batch and then freeze them for breakfasts and snacks. Let them thaw for a few minutes and then eat them cold, or you can zap them for a few seconds in the microwave and eat them warm.

How Long Will Breakfast Cookies Keep?

When you store the cookies in the fridge, they will keep for 7-10 days. When you freeze them, they will last for up to 3 months.

If you’re searching for new healthy breakfast ideas, look no further than these apple cinnamon breakfast cookies! They are full of fiber and will keep you full until lunch time. They are chewy and moist and full of nutrients to starts off your day strong!

More Healthy Breakfast Ideas:

Healthy Apple Cinnamon Breakfast Cookies

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Servings: 12 cookies
Prep Time: 10 minutes
Cook Time: 15 minutes
Total Time: 25 minutes


  • 1/2 Cup Whole Wheat Flour
  • 1/4 Cup Oat Flour, *whole wheat
  • 1/2 teaspoon Baking Powder
  • 1/2 teaspoon Salt
  • 1/2 teaspoon Cinnamon
  • 1/4 teaspoon Cardamom, optional
  • 1/2 Cup Apple Butter, *see note
  • 1/3 Cup Brown Sugar
  • 1 Egg
  • 1 teaspoon Vanilla
  • 1 Medium Apple, grated with peel
  • 1 1/2 Cup Old Fashioned Oatmeal
  • 2 Tablespoons Pepitas, optional
  • 3/4 Cup Raisins/Craisins, or whatever dried fruit you like


  • Preheat oven to 375.
  • Mix flours, cinnamon, baking powder, salt and spices together.
    1/2 Cup Whole Wheat Flour, 1/4 Cup Oat Flour, 1/2 teaspoon Baking Powder, 1/2 teaspoon Salt, 1/2 teaspoon Cinnamon, 1/4 teaspoon Cardamom
  • Stir in apple butter, sugar, egg and vanilla.
    1/2 Cup Apple Butter, 1/3 Cup Brown Sugar, 1 Egg, 1 teaspoon Vanilla
  • Add apple, oatmeal, pepitas and raisins.
    1 Medium Apple, 1 1/2 Cup Old Fashioned Oatmeal, 2 Tablespoons Pepitas, 3/4 Cup Raisins/Craisins
  • Place spoonfuls on a greased cookie sheet and smash them down to about 1/2" as they will not flatten by themselves.
  • Bake 15 min and cool on a rack.
  • Store in an air-tight container in the refrigerator.


  • You can substitute half the apple butter for oil or applesauce.
  • Store in an airtight container in the refrigerator.


Serving: 1cookieCalories: 142kcalCarbohydrates: 29gProtein: 3gFat: 2gSaturated Fat: 1gTrans Fat: 1gCholesterol: 14mgSodium: 110mgPotassium: 194mgFiber: 3gSugar: 12gVitamin A: 32IUVitamin C: 1mgCalcium: 27mgIron: 1mg
Author: Sweet Basil
Course: 100 Best Cookies Recipes on the Planet, Over 200 Favorite Easy Breakfast Recipes

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a photo of two healthy breakfast cookies stacked on each other full of raisins and pepitas