Pumpkin Cupcakes Recipe

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These pumpkin cupcakes are made with whole grain flour and no processed sugar, and you know what? They still taste delicious! (gasp!)

For those of you who read my blog regularly or follow me on Facebook, you probably know that I do not feed my son any sugar. In fact, he eats really, really clean, and I’m really really proud of that.

Clean Eating Pumpkin Cupcakes Recipe

So as I’m sure you can imagine, Halloween proves to be somewhat of a challenge every year. The older he gets, the harder it is to deal with.

But I’m a cleaver girl, so I have a few tricks up my sleeve. One of which, is this recipe. While other kids are chowing down on sugar galore, my little guy will be happy to eat these cupcakes. And frankly, so will I!


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Clean Eating Pumpkin Cupcakes Recipe

Clean Eating Pumpkin Cupcakes With Chocolate Pumpkin Frosting

Love cupcakes? Me too! These delicious goodies have more good nutrition in them than anything store bought. But shhhh!!! The kids will ever know!
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Prep Time: 20 minutes
Cook Time: 20 minutes
Total Time: 40 minutes
Servings: 16 cupcakes, approximately
Author: The Gracious Pantry


  • 1 cup canned pumpkin (not pumpkin pie filling)
  • 1/2 cup unsweetened almond milk
  • 2 large egg whites
  • 1/2 cup oil, light flavored
  • 1/2 cup honey
  • 1 tsp. pure vanilla extract
  • 2 cups whole wheat pastry flour
  • 1/4 tsp. salt
  • 1 tsp. baking soda
  • 1 1/2 tsp. ground cinnamon
  • 1/2 tsp. ground ginger
  • 1/4 tsp. ground cloves
  • 1/2 cup canned pumpkin (not pumpkin pie filling)
  • 1/2 cup unsweetened cocoa powder
  • 1/4 cup honey
  • 1/4 cup unsweetened apple sauce
  • 1 tsp. pure vanilla extract


  • Preheat oven to 350 degrees F.
  • Line your cupcake tins with cupcake papers or grease the tin itself.
  • In a large mixing bowl, whisk together your pumpkin, almond milk, egg whites, safflower oil, honey and vanilla extract.
  • In a second mixing bowl, whisk together your flour, salt, baking soda, cinnamon, ginger and cloves.
  • Whisk the flour mixture into the liquid mixture and blend well. If your batter is too thick, add a little extra almond milk (about 1/4 cup at a time until you reach a thick, yet runny consistency.)
  • Pour into tins, and place in the oven for 15-20 minutes or until a toothpick stuck in the middle of a cupcake comes out clean.
  • For the frosting, place all ingredients in a small mixing bowl, and whisk until well blended.
  • Remove cupcakes from oven, allow to cool and spread frosting over the tops.

This recipe from the Gracious Pantry archives, originally published on 10/25/2010.

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  1. Oh, yum! I can think of some kids who would LOVE those!

    1. The Gracious Pantry says:

      Sarah – Ya, I’m one of them!

  2. Wow – sounds great!

    1. The Gracious Pantry says:

      Leslie – Thanks! They were pretty yummy! Can’t wait to make another batch for Halloween!

  3. I could eat that frosting by the spoonful 🙂 The cupcakes look great!

    1. The Gracious Pantry says:

      Lauren – Ya, I won’t lie. I ate some by itself…. and it was good!

  4. Great recipe, can’t wait to try it! My son started Kindergarten this year and about once per month I have to bring in snack for the entire class, these may be next on the list! Any other ideas you have for portable, non-refrigerated, healthy snacks that will please 24-5 year olds?

    1. The Gracious Pantry says:

      Dawn – I have several muffin recipes that are really kid friendly. Those are always a hit with the kidlets.

  5. Ashlee (AshandLewPlus2) says:

    What an awesome recipe! I can’t wait to try them! I have 7 month old twins and am hoping to control their sugar intake when they get older and am so glad you give such great options to do that!

    1. The Gracious Pantry says:

      Ashlee – Thanks! Let me know how they turn out for you. They are definitely a favorite around my house!
      Adorable munchkins you have, btw.

  6. Very cute! I love that you used honey to sweeten these. For some reason, I am always cautious about the combo of honey and chocolate – it sounds slightly off to me, but I will have to give it a go!

    1. The Gracious Pantry says:

      Alisa – When I lived in Germany, there was a small company that made nothing but chocolates sweetened with honey. All I can say is, it’s a good thing I did so much walking there, otherwise, I would have had a free ticket flying home simply because I would have come home as a blimp. The combination is heaven!

  7. Have you tried using pumpkin in place of oil in brownie and cake “mixes”? Very yummo. Of course, unsweetened applesauce works, too, depending on the recipe. Applesauce tastes and “works” better in a light-colored baked good (like yellow cake), while the pumpkin is A-mazing in chocolate and devil’s food cakes, brownies–even chocolate-dipped truffles! Try experimenting with “pumpkin truffles” next… Mmm… 🙂

    1. The Gracious Pantry says:

      Charlena – YUM!! Pumpkin truffles??? Holy cow woman! That sounds incredible! You’ve got yourself a deal. I’ll try it!

  8. Tami@nutmegnotebook says:

    Oh my goodness that looks delicious! When my kids both ended up in braces at the same time it was a good excuse to give up trick or treating. We started a new tradition of going to a movie instead!

    1. The Gracious Pantry says:

      Tami – That’s fantastic! What a wonderful tradition. I’m sure the kids will continue that for a long time to come.

  9. Anna Johnston says:

    Great recipe. Honey & chocolate hey…, interesting.

    1. The Gracious Pantry says:

      Anna – I’m really surprised by how many people think the combination is “interesting”. lol. When I lived in Germany, it’s the only way I ate chocolate. It was fabulous! Must be a European thing.

  10. These sound so yummy! I was wondering if you could substitute the honey for agave nectar? It would reduce the glycemic load even more. I have to watch that.

    1. The Gracious Pantry says:

      Mary – Yes you can. I’ve started to avoid agave due to the controversy around it. But either honey or agave will work.

  11. Donna Maria Coles Johnson says:

    This is so cool? I’m curious. Has your son EVER had any sugar at all? Ever?

    1. The Gracious Pantry says:

      dM – No. Not a drop. I realize this will change in the future, especially when he gets into school. But for now, he’s refined sugar-free! (He’s had honey and agave. Just none of the white stuff)

  12. Chrystal Nelson says:

    Yum!! These are so good! Had to cut my hubby off after he ate about 6! I made them a bit smaller so I got 24 out of the recipe, knowing that it would probably be difficult to stop at just one! Yup – good idea! LOL!

    PS. Love the idea about the pumpkin truffles – can you do that one for Christmas this year? I always seem to be the one that does all the Christmas baking, and now that I’m eating clean, I need some better options 🙂

    1. The Gracious Pantry says:

      Chrystal – Yay! So happy you liked the cupcakes! 🙂 I will see what I can do about the truffles. I need to find a recipe to start with. Do you have one?

    1. The Gracious Pantry says:

      Chrystal – Thanks! I’ll give it a shot!

  13. hi!! do you think its also possible to make a cake out of this recipe?? i’m in need for a pumpkin cake recipe for halloween, and this sounds yummy…thanks for your answer!! Ulli

    1. The Gracious Pantry says:

      Ulli – Good question. It might work but you would have to experiment with the baking times and temperatures a bit. I would say…. maybe try baking at a lower temperature for a longer amount of time. I’m sure it will work, I just don’t know how long it would take to bake it. Wish I could be more help.

  14. thanks for your answer, i’ll just try it!! 😉

    1. The Gracious Pantry says:

      Ulli – Please let me know how it turns out! (I might have to make one too!!)

  15. hi!! just wanted to tell you that i made your cake, its sooo delicious (i just ate what i cut away from the top yet, but that was gooood!!)!! i doubled the amounts and baked for about 60 minutes! i’ll post pictures tomorrow on my blog if you are interested (its in german, but you can still look at the pictures) thanks again!! Ulli

    1. The Gracious Pantry says:

      Ulli – Fantastic! I can’t wait to see your photos! (I read/speak German – my family is from Stuttgart and I lived there for a year as an au pair).

  16. o0_haylo_0o says:

    my frosting didn’t come out right. I think I will try less cocoa powder next time, but i did combine the frosting I made with sugar free chocolate frosting I bought at the store and it was yummy.Thanks for the recipe!

    1. The Gracious Pantry says:

      Haylo – Next time, just add a bit more apple sauce. It should work pretty well.

  17. I just wanted to let you know that I thought the cupcakes needed a tad more salt. Like maybe 1/2 tsp instead. Otherwise, wonderful!

    And I noticed your comment to Haylo–Is there supposed to be applesauce in the frosting?? It’s not listed in the ingredients!

    1. The Gracious Pantry says:

      Selena – I try to cut down on my salt intake, so my recipes reflect that.

      I added the apple sauce to the recipe. Thanks for pointing it out!

  18. Thank you! Good to know there was another ingredient needed. The frosting was funky without! 🙂

    1. The Gracious Pantry says:

      Selena – Glad it worked out!

  19. Kelly Cain says:

    I tried this recipe and the cupcakes turned out great but I’m not sure what I did to the frosting to make it so bitter? I’m not a huge sweet tooth but it wasn’t sweet at all and I added a bit of agave to try to sweeten it but to no avail. Any thoughts on what I did wrong? Otherwise these are yummy! 🙂

    1. The Gracious Pantry says:

      Kelly – It sounds like something went wrong with the apple sauce or honey. You can always add more honey (or agave) to taste, but you may need to adjust the consistency of the frosting with a bit more cocoa powder. With this recipe, its safe to play around with amounts. You just have to readjust the other ingredients to get the texture right. Hope that helps.

  20. Sara Wittenberg says:

    Awesome! I was looking for a sugar-free cupcake recipe for my daughter’s 1 year birthday in October, and thought pumpkin would be cool, and found this! Cannot WAIT to try it!!!

    1. Anonymous says:

      Sara – Oh good! I hope you’ll enjoy them!

  21. Anonymous says:

    Sara – You can use regular, but you will end up with a much coarser and denser cupcake. You might try white whole wheat. It’ll get you a little closer to the right consistency and it can be a little easier to find in the stores.

  22. Kellymeeks5 says:

    I just made these and they didnt rise very well and are extreamly dense, any thoughts?

    1. Anonymous says:

      Kelly – did you change anything? Use a different flour maybe?

  23. Anonymous says:

    BeShrable – There is a difference in how the flours cook. But you should be able to get away with it. White whole wheat is typically and easy substitute.

  24. Anonymous says:

    Sherelyn – I’m so happy you enjoyed them! And you’re right, when you ingest that much sugar daily, you won’t enjoy something like this because your taste buds have been “altered”. Good for you for eating clean! Go girl!

  25. My husband made these for me today for my bday. SO yummy!!! I started my weight loss journey and working with my trainer in March 2011. I have been eating clean ever since. I feel fantastic! I have already decided to continue eating clean, even after I reach my goal weight. I cannot even imagine eating any other way at this point. Thank you!!!

    1. Anonymous says:

      Enj5 – Yes! That’s exactly how it should be. Good for you, and happy birthday!

  26. Anonymous says:

    Stephanie – Yay!!! Glad you enjoyed them!

  27. Sara Wittenberg1 says:

    Yeay, finally made them for my 1 year old’s birthday party yesterday, they were a hit! Already passing out the recipe to others! THANKS!

    1. Anonymous says:

      Sara – Fantastic!! Glad everyone liked them!

  28. Anonymous says:

    Melissak – Wonderful! I hope the kids enjoy them!

  29. Anonymous says:

    KitKat – That’s wonderful!!! Good for you! You’ll make memories that last a lifetime that way!

  30. April at Pivotal says:

    I would love to try making these with some protein powder. Any suggestions as to how much I should use? Thanks for putting together such a wonderful site!

    1. Anonymous says:

      April – Oh boy. I’m not really sure. I think protein powder soaks up more liquid than flour. So you’d have to replace some of the flour with protein powder and then adjust the liquid to get the right consistency. Of course, this all depends on how much you want to use. If it’s only a couple tablespoons, then I doubt you’d have to make any adjustments at all. Just add it. Let me know how it turns out!

  31. Anonymous says:

    Talisha – Oh yum! I never would have thought to use that! Thanks for the tip!

  32. Anonymous says:

    Marybeth – I’m sure it would work just fine!

  33. cytress_78 says:

    The muffins were great. The icing was a litte bitter and over sweet at the same time if that makes sense at all. I think I prefer them without the icing, although my daughter things that everything smothered in chocolate is delicious. I might try to tweek the icing a little next time. Thanks for the recipe.

    1. graciouspantry says:

      Sure! You can always add more honey…

  34. graciouspantry says:

    I’m sorry, but I know nothing about gluten free living. Try Elana’s Pantry. I believe all of her recipes are based on those same allergies, and many if not most of them are clean.

  35. graciouspantry says:

    Try using butternut squash instead. It’s a good substitute. 🙂

  36. Very addicting. These were absolutely amazing!

  37. If I use whole wheat flour do I need to adjust anything in the cupcake recipe? Also, is there any substitute for the pumpkin in the frosting recipe to make it more of a plain chocolate flavor?

    1. The Gracious Pantry says:

      Jill – You can use equal amounts of regular whole wheat, but the muffins will be more dense and coarse. I have a frosting recipes listed under my dessert category on my category page if that helps. I have 3 chocolate frostings.

  38. I might just be slow..lol but what are ground cloves? what do they look like? Where can I find them?

    1. The Gracious Pantry says:

      Samantha – I looks similar to cinnamon, only a little darker. You’ll find it in the spice aisle with all the other spices.

  39. Dawnielle says:

    I’m doing the Paleo diet and the cupcakes have all the paleo ingredients except for the flour. Can I substitute another flour like almond or coconut?

    1. The Gracious Pantry says:

      Dawnielle – I don’t recommend it. These are formulated for gluten. I’ll see if I can come up with a grain free version though.

  40. I’m new to “clean eating” and love the idea of providing healthy treats for Halloween! For the non-chocolate fans in my life (I know, right?) do you have an alternative frosting like pumpkin cream cheese frosting? Or would that be completely “dirty”? Thanks in advance!

    1. The Gracious Pantry says:

      Trisha – I don’t have one, but that’s an excellent idea. Maybe mix some pumpkin puree, sucanat or coconut sugar together and then add some cream cheese or maybe even a little butter into it. I’ll see if I can come up with something. 🙂

  41. Thanks! I look forward to what you come up with 🙂 In the meantime, I tried this recipe:
    I didn’t make the full recipe–just put in the called for ingredients to taste. My kids loved it. They also RAVED about your pumpkin cupcake! “This is so so good!! And good for you too!!!” (Ages 7 and 5) followed by cupcake devouring.

    1. The Gracious Pantry says:

      Trisha – Looks good! 🙂 Glad everyone enjoyed them!

  42. Kathy Perry says:

    Hi, I recently made your clean frosting nut butter, and substituted the peanut butter with almond butter. I have to say, it was a great recipe! However, I was wondering how long would it last in the refrigerator?

    1. The Gracious Pantry says:

      Kathy – That’s tough to say. I think it’s pretty safe to say at least a week. Maybe longer. But I’ve never kept it long term to find an exact time frame.

  43. Kathy Perry says:

    Thank you…by the way, my family and I love your recipes!

    1. The Gracious Pantry says:

      Kathy – Thanks! I’m glad you’re enjoying them! 🙂

  44. lisa florin says:

    OMG! These look so good! Cant wait to try them this weekend!! Thanks so much for all the wonderful recipes!

    1. The Gracious Pantry says:

      Lisa – My pleasure! Let me know how they turn out! 🙂

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