Soft, chewy, healthy pumpkin breakfast cookies made with nutritious ingredients, like oats, ground flaxseeds, and peanut butter. Wholesome, make-ahead friendly, loved by kids, and perfect for fall mornings.
Be sure to check out these easy gluten-free pumpkin scones and gluten-free chocolate chip pumpkin bread if you're looking for more healthy pumpkin recipes.

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"These cookies are really good. I made them for my sons 2nd birthday and him and his sister both loved them. Cookies for breakfast! I should have double the recipe like you suggested." -Ashley
Reasons to Love These Pumpkin Breakfast Cookies
- Full of fall flavors - Just like my pumpkin muffins with almond flour, these cookies have all the cozy fall flavors like warm cinnamon and pumpkin spice.
- Wholesome and healthy ingredients - You won't find any refined flours or refined sugars in this cookie recipe! Plus, they are made with whole grains and you get the benefits of fiber, protein, and healthy fats from ground flaxseeds. Now that's a healthy pumpkin breakfast cookie you can feel good about.
- Protein and fiber - Each cookie contains 6 grams of protein and 4 grams of fiber! Try these protein peanut butter banana muffins if you like protein rich baked goods.
- Easy, one-bowl - These cookies require just one bowl (less clean up) and are ready for the oven in just 15 minutes.
These really are the best soft and chewy pumpkin cookies, and just like my healthy breakfast cookies, these are so easy for making ahead and enjoying throughout the week. Perfect for eating alongside some hard-boiled eggs and fresh fruit for a well-rounded breakfast. Mornings never got easier (and healthier).
And as an added bonus, my kids love these. I'm sure the chocolate chips have something to do with it, but I do love knowing they are getting real, nutritious food to star their days. But, we do also loves these as a snack, so don't let the name "breakfast cookie" keep you from reaching for these in the afternoon!
Ingredient Notes

- Rolled oats - Also known as old-fashioned oats. If making for someone with a gluten sensitivity or celiac, be sure to use certified gluten-free oats. Although oats don't contain any gluten naturally, they may become contaminated with gluten during processing in facilities that also process wheat.
- Canned pumpkin - You should use canned pumpkin/pure pumpkin puree and not pumpkin pie filling. Make sure the only ingredient is "pumpkin."
- Peanut butter - Make sure to use drippy, natural peanut butter (peanut butter, and maybe salt, should be the only ingredient). Costco makes a great one and I also like Once Again peanut butter.
- Oat flour - I like using homemade oat flour since it's a whole grain, but if you don't have oat flour, you can use regular flour, wheat flour, or even a gluten-free flour substitute. Be sure to use certified gluten-free oat flour if needing these to be gluten free. Check out my oat flour pancake recipe for another way to use oat flour.
A complete list of ingredients and amounts can be found in the recipe card below. Here are some specific notes to help with selecting ingredients.
Clean food tips: I highly recommend organic oats. Like most grains, oats are sprayed with glyphosate. If avoiding herbicides and pesticides is important to you, choose organic.
Chocolate chips should contain sugar, chocolate, and cocoa butter. My favorite brands include Equal Exchange, Hu Chocolate, and Pascha.
Use a nut butter that contains just the nuts and maybe salt. Ensure there are no added oils or sugars.
Substitutions and Add-ins
- For a nut-free pumpkin breakfast cookie, swap the peanut butter for sun butter.
- To make vegan, use an egg substitute and use dairy-free chocolate chips.
- You can definitely play around with add-ins in this recipe. Add in some chopped walnuts or pecans or even some pumpkin seeds. Swap the chocolate chips for dried cranberries, or use both!
Step-by-Step Instructions

Step 1: Whisk together the wet ingredients in a medium sized mixing bowl.

Step 2: Add the remaining dry ingredients (aside from the chocolate chips) and mix until oats are fully mixed in and a thick "dough" as been formed.

Step 3: Fold in the chocolate chips.

Step 4: Using a spring-loaded cookie scoop, scoop balls of dough onto a prepared cookie sheet (use a heaping 2 tbsp. of dough per cookie).

Step 5: Using your hands, flatten each dough ball into a round, cookie shape. The cookies won't spread, so shape them how you'd like them.

Step 6: Bake at 350-degrees F for 12 minutes, or until edges are set and cookies are semi-firm to the touch.
Expert Tips
- This recipe makes 12 cookies, but I highly recommend you double the recipe so that you have plenty for freezing.
- The dough will be sticky, so get your hands wet before flatting/forming dough balls into a cookie shape - this will prevent it from sticking to your hands.
- Use a spring-loaded cookie scoop to easily make the dough balls. A 2 tablespoon sized scoop works best for this recipe.
- Drizzle some coconut butter glaze on the tops for extra flavor and slight sweetness.

How to Store and Freeze
Storing: Store cooled cookies in an airtight container on the counter for up to 3 days. You can slightly warm in the microwave for a soft warm cookie.
Freezing: Place the cooled cookies in a freezer container or bag and freeze for up to 3 months. These cookies freeze great, so I highly suggest making a double batch.
Recipe FAQs
Yes! They are made with wholesome ingredients like rolled oats, flaxseeds and pumpkin puree. These are naturally sweetened (no refined sugar) and contain fiber, protein and healthy fats.
If needing these to be vegan, you can easily replace the eggs with an egg substitute, like flax eggs. And ensure the chocolate chips you use are dairy free.
Yes, you can, but the texture might not turn out the same. I have not personally used quick oats, but they should still be able to be used.

More Fall Recipes To Try
If you make this recipe, please let me know what you think! I would so appreciate you leaving a star rating and/or comment below. And don't forget to share a photo on Instagram or Facebook and mention @CleanPlateMama!
Eat Clean.Be Well!
-Sara
Healthy Pumpkin Breakfast Cookies
Save This Recipe For Later!
Equipment
- 1 Mixing bowl
- 1 Baking sheet
Ingredients
- ½ cup pumpkin puree
- 2 eggs
- 3 tbsp. pure maple syrup
- ⅓ cup natural peanut butter
- 1 tsp. pure vanilla extract
- 1 cup oats (certified gluten free if needed)
- ½ cup oat flour (certified gluten free if needed)
- ½ cup flaxseed meal (also called ground flaxseeds)
- 1 tsp. baking powder
- ¼ tsp. fine sea salt
- 1 ½ tsp. pumpkin pie spice
- ½ tsp. ground cinnamon
- ⅓ cup chocolate chips
Instructions
- Preheat oven to 350-degrees F and line a cookie sheet with parchment paper. Set cookie sheet aside.
- In a medium sized mixing bowl, whisk together the pumpkin puree, eggs, maple syrup, peanut butter, and vanilla.
- Add the oats, oat flour, flaxseed meal, baking powder, salt, pumpkin pie spice, and cinnamon. Mix until oats are fully combined. Fold in the chocolate chips.
- Scoop a heaping 2 tablespoons of dough per cookie (spring loaded cookie scoop works best) onto the prepared cookie sheet. You should get 12 cookies. Slightly wet your hands and press and shape each dough ball into a cookie shape. Dough won't spread when baked, so shape them how you'd like them.
- Bake for 12 minutes, or until edges are set and cookies are semi-firm to the touch.
- Allow to cool slightly. Enjoy!
Notes
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- The dough will be sticky, so get your hands wet before flatting/forming dough balls into a cookie shape - this will prevent it from sticking to your hands.
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- Save some of the chocolate chips for adding to the tops of the cookies before baking to get that bakery style look and feel.


Carrie says
these cookies came together nicely however their flavor profile was terrible!
I'm disappointed I wasted ingredients on them.
Sara says
I'm sorry to hear you didn't like the flavor of the cookies. Appreciate you giving them and try and leaving a review!
Ashley says
Thanks for your fast response, Sara! Based on what you said, I mixed up the wet and dry ingredients separately the night before. It was easy to combine while the oven preheated in the morning.
These cookies are really good. I made them for my sons 2nd birthday and him and his sister both loved them. Cookies for breakfast! I should have double the recipe like you suggested. I used craisins instead of chocolate chips but they still thought they were amazing. Iwill definitely make these again. Thank you.
Sara says
So glad they turned out for you and your kiddos loved them... "cookies" for breakfast are the best 🙂 Thanks for letting me know how they turned out!
Ashley says
These look great! Do you think I could make the batter the night before and bake them in the morning?
Sara says
Hi Ashley - I think making the batter the day before and them making them would work just fine. I would try to let the batter sit at room temp for 30 minutes or so, just to soften so you can easily form them into the cookies shapes. Let me know how it goes 🙂 Excited for you to try them!
Mary says
These came out great. I can't eat oats so I substituted with a cup of cooked millet and all purpose gluten free baking flour. I also cannot eat eggs so I used the flax eggs and omitted the added flax seed. I followed everything else. Excellent! Thanks for the recipe!
Sara says
Thanks for sharing and so happy to hear they turned out with the substitutions you needed!