Breakfast Cookies

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Start the morning right — with cookies! Bake all the goodness of whole grains, oats, dried fruit, and nuts into a portable breakfast cookie.

Breakfast Cookies

My husband leaves for work before most of the household is awake. He grabs a cup of coffee and a Balance bar and hits the road. While good sales on protein bars are possible, I am on the hunt to find a more economical, yet still sustaining option.

I took my Trail Mix Cookies and tweaked them a little recently. I even experimented with coconut oil, a first for me. The result was a super tasty cookie. They taste too good to be healthy. So, I need to revisit the ingredient profile and make sure.

Whole wheat pastry flour can usually be found in the bulk section of your health food store. If you can’t find it, you can substitute unbleached or whole wheat flour.

I bake these in big batches and stash them in the freezer so that we have breakfasts made in advance. Check out this breakfast freezer cooking plan that includes these cookies. Spend a morning in the kitchen and have a month of breakfast to freeze.

Take your freezer cooking to the next level with my cookbook Not Your Mother’s Make-Ahead and Freeze Cookbook.

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breakfast cookies stacked on china plate
Breakfast Cookies
Prep Time
10 mins
Cook Time
20 mins
Start the morning right -- with breakfast cookies! Bake all the goodness of whole grains, oats, dried fruit, and nuts into a portable breakfast cookie.
Course: Breakfast, Dessert
Cuisine: American
Keyword: breakfast cookie
Servings: 36
Calories: 106 kcal
Author: Jessica Fisher
  • 1/2 cup honey
  • 3/4 cup brown sugar
  • 3/4 cup applesauce
  • 2 eggs
  • 2 teaspoons vanilla
  • 2 cups rolled oats
  • 1 1/2 cup whole wheat pastry flour
  • 1/2 cup ground flax seed meal
  • 1/4 cup dried cranberries
  • 1/4 cup dark chocolate chips
  • 1/4 cup pepitas
  • 1/4 cup sunflower seeds
  • 1/4 cup chopped nuts
  • 1 teaspoon baking soda
  • 1 teaspoon salt
  1. Preheat the oven to 350°. Line baking sheets with silpat mat or parchment paper.

  2. In a large mixing bowl, combine honey, sugar, and applesauce. Blend well. Beat in the eggs and vanilla.

  3. In a second large mixing bowl, combine the oats, flour, flax seed meal, dried cranberries, chocolate chips, pepitas, sunflower seeds, nuts, baking soda, and salt. Stir well.

  4. Add the wet ingredients to the dry, and stir until well combined.

  5. Drop the batter by tablespoons onto the prepared baking sheets. Bake 10-15 minutes or until set. Cool on rack.

  6. Store cookies in an airtight container.

Recipe Notes

Nutritional values are approximate.

To freeze: cool cookies completely and store in an airtight container in the freezer for up to 6 weeks.

Nutrition Facts
Breakfast Cookies
Amount Per Serving
Calories 106 Calories from Fat 27
% Daily Value*
Fat 3g5%
Saturated Fat 1g6%
Cholesterol 9mg3%
Sodium 103mg4%
Potassium 89mg3%
Carbohydrates 18g6%
Fiber 2g8%
Sugar 10g11%
Protein 3g6%
Vitamin A 15IU0%
Vitamin C 1mg1%
Calcium 20mg2%
Iron 1mg6%
* Percent Daily Values are based on a 2000 calorie diet.


About Jessica Fisher

I believe anyone can prepare delicious meals—no matter their budget.

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  1. Looks great for my runner food “snob” husband! 😉

  2. Jill says

    These look great!

  3. Terry says

    I made these today but used unsweetened applesauce in place of all of the oil. The applesauce adds extra flavour and tang as well as making this a low-fat cookie. I added dark chocolate chips, dried cranberries, slivered almonds and shredded unsweetened coconut. Talk about delicious! My kids and I can’t stop eating them.

  4. Candi says

    Looks delicious! I made a pumpkin oatmeal cookie with dried cranberries last year. It was pretty good too.

  5. Hi Jessica,
    I just put my daughter on a Gluten Free diet for her eczema and it’s helping a lot. What do you suggest I replace the whole wheat flour with? I can use all the rest of the ingredients.

    • Jessica says

      That would be a great question to ask over at Lynn’s Recipe Adventures. We aren’t doing gluten free, so I have no idea. But, Lynn does!

    • Hannah says

      @Kristen, Hey Kristen, I eat GF as well, and I was just thinking I’d probably replace the 1 1/2 cup whole wheat flour with:

      3/4 c almond flour
      1/2 c brown rice flour
      1/4 c high protein flour such as millet, quinoa, etc

    • Nicole P says

      Rice flour works well for us!

  6. yum! Who wouldn’t want cookies for breakfast. What could I use in replace of the flaxseed? more flour?

  7. Kiersten says

    I needed a healthy cookie quickly today. I remembered your post on these and they were great! Thanks.

  8. Cassie says

    I was looking for something nutritious to give my 18-month-old in the mornings because other than his usual plain Cheerios. I tried these out, but with a few changes: omitted the flaxseed because I didn’t have any, substituted 1/4c. homemade unsweetened applesauce for 1/4c. of the oil, cut back by 1/4c. on the sugar, and added sesame seeds, sunflower seeds, dried cranberries and orange zest. They turned out great, but next time I’ll definitely add more orange zest. It was such a great addition! And the dark chocolate sounds great…might add that too. Thanks, Jessica, for a wonderful recipe!

    • Jessica says

      @Cassie, thanks for letting me know. Reminds me I need to make a few batches. 🙂

  9. Jenny says

    Finally got around to making these today, and they are wonderful. Kids love them, hubby loves them. He asked me to make some for him to take in to work. Praise doesn’t come much higher than that. We made a couple of quick subs to fit what we had in the house. Instead of flax meal, just used more oats. For the flavor bits, we used choc chips, coconut, sliced almonds, pepitas, and raisins.

  10. Sarah says

    HI! Here’s another variation, for anyone who’s interested. I omitted both the honey and the flaxseed. I think by omitting basically equal parts dry and wet ingredients, it worked fine in the end result. I just didn’t have either item in my pantry. This might help the people who were asking about a substitute for the flaxseed.
    Jessica, I also cut the sugar to 1/3 c., which I think makes them a little healthier. My kids and husband all liked them, so it was fine, but my (processed-foods-eating) neighbor kids didn’t like them.
    Thanks for a great recipe for my own little Hobbits!

  11. OMG! These are perfect for DD’s lunchbox. Quick question – Can I substitute the coconut oil with regular canola oil?

    • Jessica says

      @Prerna, yes, that should be fine. The texture will be a little different.

  12. Jill says

    This is my third time making the cookies, all a little different each time. What a fantastic recipe and it is fun to play with. Soooooo good with a cup of coffee in the morning.

  13. Mandi says

    Do you think these would work with old fashioned oats as opposed to quick oats? I’m really searching for some breakfast options I can make ahead!

    • Jessica says

      @Mandi, that should be fine. The texture will be a little rougher. But, if you’re used to using those in other cookies, it will be fine.

  14. lacey says

    can these be frozen

    • Jessica says

      Yes. Wrap them well and stash in the freezer. Yum!

  15. Peggy says

    What is pepitas??

    • Jessica says

      Pepitas are pumpkin seeds w/o the outer coating. I buy mine at Trader Joe’s

  16. This recipe looks delicious! I’ve been trying with my own granola bar recipe, but having trouble with the chewy vs. crunchy (can’t quite get either one, lol). I think I’ll put that on the back burner and try these instead. Thanks so much!

    • Jessica says

      I’m struggling with those also! These are a sure thing.

  17. Stacy says

    I made the breakfast cookies yesterday and they were very good. Thanks! I used everything you said except I didn’t have whole wheat pastry flour, so I used white pastry flour + white whole wheat flour (2:1), and I substituted sunflower seeds for the pepitas. I was also thinking of ways to make this a bit healthier, so the comments above were very helpful. I would like to cut down on the sugar and honey substantially. I have hardly used the coconut oil I bought awhile back because I wasn’t sure what to use it in, but it was great in these cookies! I love the flavor and next time I might add some coconut flakes too.

  18. Candy J. says

    I’m going to try these for me picky 4 and 6 year old boys!

  19. Shirlene says

    Made these cookies today and yum! 4 yr old is eating them like no tomorrow. I did modify a bit like some of the ladies above and cut the brown sugar to 1/2 cup light brown and replaced the oil with unsweetened applesauce, used raw wheat germ in place of flax seed meal, used whole wheat flour and Iodized sea salt. These came out like a soft pillow. I thought they would spread out and be a bit crispy after seeing the picture (are they suppose to come out crispy?). I will definitely make these again with variations on the add in’s. I used dried cherries , semisweet choc chips and almonds, taste like a choc covered cherry! Thanks for sharing.

    • Jessica says

      @Shirlene, changing the sugar and oil and other items will definitely change the texture. 😉

  20. Carla says

    Made these last night and of course did not wait to test them. Everyone was good with them but I doubt they will eat them for breakfast–I might. We will definitely make more but use them as a healthier/filling snack. I used canola oil since that is what I had. Due to lack of sesame seeds and a nut allergy I used toasted wheat germ (my stand in for “nutty” taste) and sunflower seeds. I saved my dark chocolate chips since I want to use them in one of your other recipes and used mini choc chips instead. 😉 I’ll definitely track down some sesame seeds. What difference in texture does coconut oil make as I’ve never used it—that and I’m leary due to nut allergy (although I haven’t seen a problem with coconut before). I might try to cut back on the oil a smidgen as I use flax a lot and the oil in it often lends to a decrease in other recipes . .. to ponder.

  21. I just tried this recipe over the weekend and they turned out so well! Everyone, including my twin 15 month old girls love them (**I left out the nuts**). I will continue making these as a healthier version of a cookie for my household. Thank you so much! 😀

  22. Leah says

    These were great, Jessica! I didn’t have WW pastry flour so did half AP and half WW, subbed raisins for cranberries, and left out the nuts and flax seed. It is a great, versatile recipe that seems really open to adding and subtracting depending on what you happen to have in the cupboard. Also, since you only need 1/4 cup of each add-it, it would be a great recipe to use up the little left-overs that seem to float around this time of year!!

  23. Emily says

    I made these tonight & they are delicious! I used what I had on hand for the trail mix combination, which was sesame seeds, chopped walnuts, sunflower seeds & chocolate chips. Yum! Thanks for the recipe!

  24. Ellen says

    I’ve made these several times. Each time there have been slight variations. Loved the original recipe. Started making changes just for fun. Added coconut (because I love it), then reduced the sugar, because of the coconut’s sweetness. Changed around dried fruit for fun and variety – have used apricots and cherries. So happy to have this recipe and it’s versatility. Thank you!

    • So glad you’re enjoying them. The last time I made them, they were too sweet. We’re slowly losing our taste for sweetness. Yay!

  25. sona says

    anyplace online to figure the nutritional value?

    • Look up nutritional calculator and you’ll get lots of apps. Sometimes the results vary from app to app. FYI: the nuts, chocolate, and coconut oil skew it pretty high on the fat end. Enjoy in moderation.

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