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 clever 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!

More Halloween Cupcake Recipes

Pumpkin Cupcakes Recipe Card

Copyright Information For The Gracious Pantry
Clean Eating Pumpkin Cupcakes Recipe

Healthy 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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Course: Dessert
Cuisine: American
Prep Time: 20 minutes
Cook Time: 20 minutes
Total Time: 40 minutes
Servings: 16 cupcakes, approximately
Calories: 184kcal


Cupcake Ingredients

  • 1 cup canned pumpkin (not pumpkin pie filling)
  • ½ cup unsweetened almond milk
  • 2 large egg whites
  • ½ cup oil (light flavored)
  • ½ cup honey
  • 1 tsp. pure vanilla extract
  • 2 cups whole wheat pastry flour
  • ¼ tsp. salt
  • 1 tsp. baking soda
  • tsp. ground cinnamon
  • ½ tsp. ground ginger
  • ¼ tsp. ground cloves

Frosting Ingredients

  • ½ cup canned pumpkin (not pumpkin pie filling)
  • ½ cup unsweetened cocoa powder
  • ¼ cup honey
  • ¼ 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 ¼ 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.


Please note that the nutrition data given here is a ballpark figure. Exact data is not possible.


Serving: 1cupcake | Calories: 184kcal | Carbohydrates: 28g | Protein: 3g | Fat: 8g | Saturated Fat: 2g | Polyunsaturated Fat: 4g | Monounsaturated Fat: 2g | Sodium: 125mg | Potassium: 163mg | Fiber: 3g | Sugar: 14g | Vitamin A: 3578IU | Vitamin C: 1mg | Calcium: 28mg | Iron: 1mg

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

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  1. 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!

  2. Anonymous says:

    Stephanie – Yay!!! Glad you enjoyed them!

  3. 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!

  4. Anonymous says:

    Melissak – Wonderful! I hope the kids enjoy them!

  5. Anonymous says:

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

  6. 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!

  7. Anonymous says:

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

  8. Anonymous says:

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

  9. 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…

  10. 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.

  11. graciouspantry says:

    Try using butternut squash instead. It’s a good substitute. ๐Ÿ™‚

  12. Very addicting. These were absolutely amazing!

  13. 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. 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.

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

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

  15. 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. 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.

  16. 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. 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. ๐Ÿ™‚

  17. Thanks! I look forward to what you come up with ๐Ÿ™‚ 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.

  18. 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. 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.

  19. Kathy Perry says:

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

  20. lisa florin says:

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