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Easy, Healthy Pumpkin Cookies Recipe

Want to get a super food like pumpkin into your family? Put it in cookies!

My husband, who doesn’t even like pumpkin, loves these healthy pumpkin cookies. The whole wheat version of the recipe hardly tastes different than the unhealthy pumpkin cookie recipe I started out with, and they remain quite easy to make.

It’s one of those recipes that I’ve had saved on my computer since long before I started blogging, because so many people ask for it after I bring the cookies to an event!

Healthy Pumpkin Cookies 1
Get this recipe, updated and improved with tons of FAQs, in the eBook “Smart Sweets,” along with 29 other delicious desserts that won’t make you feel guilty! Click HERE for a table of contents.

Of course, I was tickled to see that the saved version still had shortening and only one cup of whole wheat flour in it.

I’ve tweaked it a lot just like my healthy pumpkin muffins which even became gluten-free pumpkin muffins. (UPDATE: It took some testing, but I’ve perfected the gluten-free version of these cookies!)

If you’re a die-hard soaker, I’ll be sure to update this post after I try the cookies with sprouted flour once we’re back to grains this fall. UPDATE: Sprouted flour works wonderfully!

healthy pumpkin cookies

When starting with a white flour, Crisco-based recipe, I always used to move up slowly. My initial healthy upgrades include some baby steps you may want to take if your family is still pretty used to white flour and you’re trying to upgrade your own dessert recipes:

  • Substitute ground flax seed (also called flax meal) for some of the fat. Substitute using a 3:1 ratio, meaning you can pull out 1/2 cup of the shortening and add in 1 1/2 cups of flax meal. It sounds like a lot, but it works out and is very tasty. (Be sure to understand how to store flax so you don’t let it go rancid!)
  • Sub butter for the shortening. Do this one at the very least! Then throw away your shortening can!
  • Reduce the white sugar by up to 1/2 cup. Better yet replace some of it with a healthier sweetener like sorghum syrup or maple syrup.
  • Sub in one cup of whole wheat flour for one cup of the white flour.

That’s how I started, and then I just kept making changes and realizing the final product didn’t change all that much. And I landed all the way to here –>

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Whole Wheat Pumpkin Cookies

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 5 from 1 review
  • Author: Katie Kimball


With two variations using either raisins or chocolate chips, you can truly make these seasonal pumpkin cookies be a totally different experience. I rarely run into anyone who doesn’t love them.


Units Scale

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  1. *If using spelt flour, make up the dough and allow to rest overnight in the refrigerator to allow the spelt to soak up the liquid.
  2. Preheat Oven to 350°
  3. Cream fat and sweetener.
  4. Add pumpkin, eggs and vanilla; beat well.
  5. Stir together flour and next 6 dry ingredients.
  6. Add to batter; mix well.
  7. Stir in choc chips and nuts.
  8. Drop rounded teaspoonfuls two inches apart on a greased cookie sheet.
  9. Bake for 15 minutes.
  10. Makes 6 – 7 dozen cookies.


Use half the 29 oz. can and freeze the rest for another batch – it’s only 20 cents more than the 16 oz. You could also put pumpkin in soups, chili, and spaghetti sauce as extra nutrient boosters. Try my Simple Cabbage Soup, healthy pumpkin muffins, or 20 Ways to Use up Leftover Pumpkin if you’re still trying to finish the can!

If you can make your own homemade pumpkin puree, there’s no comparison in these cookies. My preferred method is real pumpkin and the honey, which make the cookies so fluffy and sweet, you’ll be shocked there’s so little sweetener. Even non-real-food eaters ask for the recipe when I bring them to share made that way.

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Healthy Pumpkin Cookies

Perfect for a Halloween party, Thanksgiving dinner, or potluck at your kids’ school, healthy pumpkin cookies will be a huge hit! The recipe is so simple, too, that your kids will love helping you out in the kitchen. This is a huge batch, but the cookies freeze excellently and are even good right out of the freezer (or thaw in half an hour on the countertop).

This post contains affiliate links to Amazon, Vitacost, Real Plans, and others from which I earn a commission. See my full disclosure statement here.

Unless otherwise credited, photos are owned by the author or used with a license from Canva or Deposit Photos.

59 thoughts on “Easy, Healthy Pumpkin Cookies Recipe”

  1. Thanks Katie! Loved these. I started with making your pumpkin pie oatmeal and had leftover pumpkin so then made these. It made a huge batch so we have plenty frozen for later. I liked using the ground flax seed. Would using unsweetened applesauce work for some of the fat? I saw that recommended in one of your brownie recipes in your e-book and have a few (okay, a lot) more weight to lose from my last pregnancy.

    1. Katie Kimball @ Kitchen Stewardship

      Applesauce tends to work pretty well to replace fat in many recipes – although I can’t remember if I’ve ever tried it with cookie DOUGH but more likely quick bread or muffin BATTER – could be different. That said – if you want to lose weight, it’s the grains and sugars, in my opinion, that you’ll want to cut…these cookies are pretty awesome on how low you can go with honey!
      🙂 Katie

  2. I just made these and am fairly new at using products beyond traditional flour, white sugar, etc… Here is what I used
    Substituted 1/2 the sugar for Coconut Palm
    Subbed 1 c almond meal and
    1 c coconut flour for 2 of the c of wheat flour
    Used all Coconut Oil
    Added about 1/2 c shredded coconut
    Added some rolled oats- 1 c or so

    Myi think I’m in LOVE!!!

    Not sure if anyone else has ever tried a good “blop” of pumpkin in their coffee, but it is so yummy with a tsp of coconut sugar and some coconut milk (or half and half if your feeling like breaking all the rules)

    Thanks for the recipie!!!

  3. Our three daughters are spending some time with their grandparents tomorrow morning while I attend a meeting at our church…what to make and share at both places??? Why not a batch of 70-80 cookies!!! 🙂 These are AMAZING….I wonder how many will be left come morning time!! hee!hee!
    Thank you, Katie, for all you do!!!

  4. I made with whole wheat flour instead of white whole wheat and they are really good! I put chocolate chips in but I’m finding I like the ones that didn’t get any chips in them better!
    The name for these should be “Addictive 100% whole wheat pumpkin cookies”!!!!!

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  6. Incase anyone is interested I subbed half the butter with unsweetened applesauce with good results!

  7. I was on and clicked on a link titled “Do Bloggers share to much?/Do we all?”

    and ended up here. could you give me a link to that particular article.

    1. Kitty,
      Whoops! thanks for letting me know of the mistake – here’s the article:

      Alsok, pardon my delay on the reply – I got behind on comments while finishing up my second edition snacks ebook… 🙂 Katie

  8. Made these today for a housewarming party. They are delicious! I used half coconut oil, half butter and home-sprouted flour. I didn’t add any add-ins, but I did use twice as much spice as called for and I dusted the tops with more spice. They came out soft, fluffy, chewy, perfect 🙂 Thanks!

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  10. Katie,
    Do your kids tolerate the flax very well? I like to bake with flax for the health benefits but can’t use nearly the amounts recommended as a fat substitute because it gives my kids (6, 4, and 2) the runs. They tell me their tummies don’t hurt; they feel fine, just visiting the potty a lot more. I figure they just can’t handle all that fiber, plus the whole grains. I’ve been making a lot of muffins lately, and for a batch of 24 muffins, about 1/4 cup of flaxmeal is enough.

    1. Sarah,
      I would have noticed it in my daughter when she was in diapers, but I didn’t. Hmmm…good question, though

  11. I make a pumpkin cookie very similar to this that’s a bit more frugal. I add yogurt in place of the eggs (allergy) and some of the butter. They turn out just as addicting…and a bit fluffy too. So yummy! 🙂

  12. Hi, I found this recipe while searching for something wholesome to make with fresh pumpkin puree. I made them last night, and while they were very delicious, they were super fragile! You can’t handle them at all without them falling apart. They aren’t dry, just fragile. I’ve never had this problem with other cookies. I didn’t see any other comments about this, and I’m wondering if I did something wrong. I followed the final “healthier” version of the recipe, and the only things I did differently are 1) I halved it, 2) I used 50/50 butter and cocount oil because I didn’t want to use up all my good butter, 3) I used whole wheat pastry flour instead of white whole wheat, 4) I used 75/25 sucanat to honey because I ran out of sucanat, and 5) I didn’t have any allspice, so I left that out. None of those things seem to me like they’d make the cookies so delicate, but I guess I don’t know!

    1. Kristin,
      At first I thought maybe the fresh pumpkin, but I have a friend who only uses her own pumpkin puree, and she loves these cookies. Unless yours had a great deal more (or less?) water content, that shouldn’t be it. The pastry flour, on the other hand, could be the culprit. I’ve not see a lot of cookie recipes that call for pastry flour, mostly only muffins, cakes, pancakes… At least they taste good! If you make them again, I’d use white or red hard whole wheat. 🙂 Katie

    2. I made cookies for my grandkids with a hundred percent whole wheat pastry flour. it worked just fine. the only time I have trouble with fragility in baked goods is when I don’t use eggs. one time in my teens I forgot the eggs in a boxed cake mix.

  13. Renee Kenyon

    I made 1/2 the recipe and did 1/2 butter and 1/2 coconut oil.
    I also used honey instead of sucanat (since I don’t have any) and they are great! (Since it was 1/2 a batch I used 3 oz which is 1/4 cup + 1 TBSP honey instead of 3/4 cup sucanat)
    I made your chocolate chip cookies with honey instead of the sugar/brown sugar and they were awesome too! (3/4 cup honey)
    Oh, and I just noticed I was supposed to use the white whole wheat…used regular whole wheat and they seem fine..somehow I think the honey makes them extra fluffy! Thanks!

    1. Renee,
      Thank you so much for trying this – for some reason I’d been hesitant to try honey in cookies. Great news that it works! 🙂 Katie

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    1. KJ, Not yet, but I’ve done practically all my other pumpkin recipes with sweet potato. I feel nearly sure it would be great! 😉 Katie

  15. I made the healthyest version with raisins and they are so good, my kids like them and I have not found too many healthy cookie recipes that they actually like, so THANKS!

  16. April Harris

    These sound really good and I love how you have provided all the variations – fantastic!

  17. I just made these this week, the healthiest version, and they are very good. I’m sort of considering adding back another 1/4c to 1/2c of sucanat though to make them closer to the level of sweetness I usually expect from a cookie. They are still good with 1.5 C sucanat, but I find that sucanat is already less sweet than refined sugar and I think the whole wheat flour and/or the flax seeds give it that “healthy” taste. although, that being said, my boys love them the way they are and I don’t feel like I’m really compromising anything to let them eat a couple for a snack or as dessert.

  18. So do I understand this right… You would use 1 1/2 cup of fat AND 1 1/2 cup flax meal? Just want to be sure so I don’t mess these up later today. Thanks?

    1. Carrie,
      Looks like I wasn’t into my comments in time to help you, but yes, 1 1/2 cups of each. I know it seems like an unbelievable amount of flax meal, but it works!
      Hope yours turned out yummy!
      🙂 Katie

  19. These cookies were a great balance between healthy tasting and treat filled. I substituted the shortening–splitting the difference between butter and flaxseed meal. You couldnt tell the difference and the cookies turned out super soft and moist. The recipe makes plenty to enjoy now and freeze some for later. That is so helpful when feeding a large family! Thanks for a great recipe!

  20. Thanks, Katie. I think I should’ve just frozen the cookies, rather than the dough — next time! 😉

    Thanks for your quick response.

  21. Although, I still will refuse to use shortening…I most certainly have to give these a bake very soon. I love cookies with squash…and lucky me…so does my Hubby ;o)

    Flavourful wishes,

  22. Hi! Cookies are delicious. However, I’m not sure if they’re a little floury tasting, or if it’s just the pumpkin flavor sabotaging itself as flour? Has anyone else experienced this? My son can’t eat enough of them, so maybe it’s just me!

    I’m wondering if I can freeze the dough, and if so, how long will they last in the freezer?

    Thanks for the recipe!

    1. Kristin,
      You know, I don’t know that I’ve ever frozen the dough because the cookies themselves freeze perfectly, but I would say with 99% certainty that it would freeze great. The cookies are still good even if they’re forgotten for, say 6-12 months! 😉 Katie

  23. Made a half batch this weekend for a family get together (7 people) and they were all gone by the end of the afternoon. I do have to admit while I halved the recipie I still included 1 cup of chocolate chips…actually 1/2 cup chocolate chips and 1/2 cup butterscotch chips. “so addicting” was a comment herd multiple time and my daughter requested I make them again. I used the flax sub. and it turned out great! Now I need to find something to do with the rest of the ground flax

    1. “Now I need to find something to do with the rest of the ground flax”
      Chuck a spoonful into the dough every time you make bread, and/or sub flaxmeal gel for eggs when you make cornbread (1 T. flaxmeal stirred into 3 T. hot water & allowed to cool). Tastes great.

  24. Where do you find white whole wheat flour? My local grocery store doesn’t stock this. The cookies look delicious!

    1. Becky,
      King Arthur flour is the brand I see most often in the store (ours is Meijer in the midwest). You can also order it through a natural foods catalog; Montana something-or-other, Chief maybe, is another chemical-free brand. Good luck! 🙂 Katie

  25. if i chose to use fresh pureed pumpkin, as I have it in the freezer, how could I measure to equal 16 oz canned?

  26. Bet these would be great with freshly baked pumpkin:

  27. Have you ever made a half batch? It looks like you could just cut all the ingredients in half but I know that doesn’t always work well. I may try it tomorrow because I don’t know if I need 70 cookies in my house, healthified or not.

    1. Katie @ Kitchen Stewardship

      Yes, all the time! The recipe card in my box even has those notes for half quantities written in. 🙂 Katie

    1. Megan,
      “Miss Music” is right; I never use shortening anymore, but it’s a good example of how to adapt a former favorite recipe for real food. I did make a note by the shortening so people aren’t confused, though, thank you. 🙂 Katie

  28. Wow! These are so good! I made them gluten free and egg free(used cornstarch instead of the eggs). Thanks for such a great recipe. I wanted to bake today because it is finally somewhat cold here in CA, these were perfect and made the house smell great. So light and fluffy….I think I could eat the whole batch, but I won’t. Thanks again!

  29. Incredible! I just made some cookies from a very similar recipe this morning! Except I used a buttercup squash, and added dried cranberries instead of the nuts and chips. Both of which were experiments on my part, and they turned out GREAT! The buttercup has such a mild flavor, the spices stand out more. I’m not sure I’ll ever go back to pumpkin!

  30. Esther Kingfisher

    I think I’ve made the original recipe already, and cut down on the sugar, but now I’m going to try your other great alterations. 🙂

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  32. Thanks, I love pumpkin recipes! I made your cabbage soup the other day and it turned out great! I’m going to try and make these this weekend.

  33. These look really good. I think I can handle 1 1/2 C sugar for that many cookies! 🙂 Thanks for the recipe. I think I’ll have to make some for our after church snacks this next week!

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