I make these every fall (okay, since last fall) and they’re always a hit. Fall doesn’t really start for me until I make these babies, and I’ve finally accepted that my favorite season is over and soon enough the leaves will change colors and I’ll have to start wearing pants (unfortunately).

I make these using almond flour, a healthy dose of anti-inflammatory cinnamon and local, raw honey. The frosting is made from both grass-fed cream cheese and butter and local maple syrup, making the frosting extremely nutrient dense; much more so than the junk you find in the store that’s loaded with hydrogenated vegetable oils, high fructose corn syrup, and refined sugar from GMO sugar beets. If you’re looking for a healthier fall cupcake recipe, this is it!

Pumpkin Cupckaes with Maple Cream Cheese Frosting
Try these healthy paleo pumpkin cupcakes with maple cream cheese frosting! Fall doesn't really start for me until I make these! So good!

Pumpkin Cupcakes with Maple Cream Cheese Frosting

I make these pumpkin cupcakes using almond flour, a healthy dose of anti-inflammatory cinnamon and local, raw honey. The frosting is made from both grass-fed cream cheese and butter and local maple syrup, making the frosting extremely nutrient dense; much more so than the junk you find in the store that’s loaded with hydrogenated vegetable oils, high fructose corn syrup, and refined sugar from GMO sugar beets. If you’re looking for a healthier fall cupcake recipe, this is it!
5 from 1 vote
Prep Time 20 minutes
Cook Time 25 minutes
Total Time 45 minutes
Course Dessert
Cuisine American
Servings 12 servings
Calories 471 kcal


  • 1 cup organic pumpkin canned
  • 2 cups almond flour
  • 1/2 cup raw honey
  • 2 eggs
  • 1/2 cup milk
  • 2 tbsp cinnamon
  • 1 tsp baking soda

Frosting ingredients:

  • 1.5 cups cream cheese cold
  • 1/2 cup butter cold
  • 1/2 cup maple syrup

Paleo Version:

  • 1 cup coconut butter
  • 1/4-1/2 cup of maple syrup depending on how sweet you like it


  • optional: coconut sugar to sprinkle on top (if you want to make them fancy)
  • Directions:
  • Preheat oven to 375.
  • Combine all ingredients in a blender or food processor. You can mix by hand, but I prefer to blend it. It makes the almond flour finer and provides a better, smoother texture for the cupcakes. Less grainy.
  • Pour the batter into 12 muffin tins.
  • Bake for 25 minutes, or until a toothpick comes out clean.
  • Combine all ingredients in a large bowl.
  • Mix until completely smooth.
  • Pipe on cooled cupcakes.


Make sure you let the muffins cool down completely otherwise the frosting will run right off them. 


Serving: 1gCalories: 471kcalCarbohydrates: 36gProtein: 8gFat: 34gSaturated Fat: 13gCholesterol: 79mgSodium: 285mgPotassium: 162mgFiber: 5gSugar: 27gVitamin A: 3850IUVitamin C: 1.2mgCalcium: 130mgIron: 1.8mg
Keyword cupcakes
Tried this recipe?Let us know how it was!


  1. Somewhere I just saw there was 1/2 cup milk missing from a cupcake recipe. Is it thisPumpkin Cupcake recipe?

    • dani stout Reply

      Yes! Oh my goodness I thought I added it, I will do that now. Thanks for the reminder!

      • Dani, help! I have these mixed up and the only deviation from your recipe is I used Coconut Flour. It is not the consistency I have experienced for cupcakes. It is not runny at all. I added another 1/2 of almond milk but still graham cracker crust consistency.

        Hoping to have these with dinner tonight; big change from our normal sugary desserts!

        Thank you!

        • dani stout Reply

          Oh no! Coconut flour is COMPLETELY different! It is VERY dry and requires A LOT more liquid and eggs. I haven’t tested it with coconut flour. With two whole cups of coconut flour you would need a very large amount of liquid and eggs, you may need to add until you get the desired consistency, but it would make a lot more than 12 cupcakes.

          • Thank you! I am a life long learner so here is another lesson!

    • dani stout Reply

      I haven’t tested it with regular flour since I don’t eat wheat but I don’t think it would make that much of a difference.

  2. Yum–sounds delicious, but I am allergic to eggs 🙁 Have you tried this recipe with an egg substitute?

    • dani stout Reply

      I get it from my farmers market but if you can’t find it, organic is fine.

  3. Do you think I could use a cup of almond flour and a cup of brown rice flour (simply in order to make the almond flour go further)? I am not sure of the exchange. Would I need to reduce the liquid?

    Thanks for the recipe! I am excited to try it!

    • dani stout Reply

      I am actually not sure, I haven’t tested with rice flour. Actually, I’ve never used rice flour. If you do it please let me know how it turns out.

  4. Is almond meal and almond flour interchangeable? I have almond meal from TJ’s, but I’m not sure what to use it for. Help?!

    • dani stout Reply

      You can use it, but it won’t provide the same texture. I used the almond flour I linked to which is very fine. You could try to blend it a lil to make it finer, that might help.

  5. Every fall I make homemade cupcakes with my nieces and nephew. I’m so excited to introduce them to the ingredients in this recipe and open their minds to healthier options, especially with treats. I don’t plan on changing a thing. Many thanks for this unique and exciting blend of flavors.

  6. Do you think I could sub heavy cream or coconut milk for the milk? I don’t have any on hand, but really want to make these! They look delicious 🙂

  7. Going to be really hard to find locally sourced maple syrup around Texas I’m afraid… What I like about this is that it is corn free!

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    • dani stout Reply

      Thanks! I actually do not since I’m against counting calories and/or carbs.

  9. Hey there! I’m planning on baking these this weekend..yay! I’m just wondering, is this fresh pumpkin, canned, pureed??


    • dani stout Reply

      I used the kind I linked to in the article but you can use whichever you like or have on hand.

  10. Do you think these would be terrible(or even work) if made with sweet potato instead of pumpkin? Got a pumpkin allergy in the house 🙂

    • dani stout Reply

      I think so, as long as you cooked and mashed the potato. Let me know!

  11. Do you think I could make these with all purpose gluten free flour instead of almond flour? And add a little xanthan gum.

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  13. Just made these again tonight. They are so delicious! I added vanilla paste, a little salt, and used allspice for part of the cinnamon. They were just delicious. Thank you!

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  16. I just made these – deelish! I subbed 1/2c coconut flour for 1c of almond flour as I ran out, but added an extra egg and one tsp baking powder and they turned out just lovely.
    I found the frosting wasn’t sweet enough, and as maple syrup is ridiculously expensive here (South Africa), I threw in a couple tsp of artificial sweetener too.
    Will definitely be making these again!

    • dani stout Reply

      Yay I’m glad you liked them! I’ll have to try ’em with the coconut flour. Thanks Tess!

  17. Have you ever tried buttermilk in this recipe? Buttermilk has nutritional value that is worth using in recipes.

  18. I made these yesterday to take to a group I facilitate and the men loved them! Fortunately I had some leftover to bring home! We love love love this recipe. Have you experimented with using this recipe with a bundt cake pan? I am trying to figure out what adjustments I might need to make. Thanks again for sharing!

    • dani stout Reply

      Yay I’m glad you liked them!

      I haven’t made this in a bundt pan but I often make cakes out of my (and others) cupcake recipes. I think it would turn out well. Let me know if you try it!

  19. Hmm just wondering if they turn out dry bc they dont have butter or oil? I really want to make for my daughters bday today!

    • dani stout Reply

      They weren’t dry for me. But they were much more dense than a traditional cupcake because of the pumpkin so if you’re looking for light and fluffy these aren’t it. Good luck!

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  21. For storage purposes how long will they last if refrigerated? Also, if refrigerated best to not apply icing (apply it at time of eating)

  22. I just made these, made a special trip to the store to get ingredients and as I was taking them out of the oven they still felt quite soft and then I realized I misread 1 cup for 1 can of pumpkin! Oops! Hopefully once they cool, they’ll stiffen a little!

  23. my icing is quite runny…is this normal?? any ideas how to fix this if it isn’t normal…?

    • dani stout Reply

      Sorry – was looking at the wrong recipe. That’s not normal. You could decrease the maple syrup and increase the cream cheese – runniness shouldn’t happen.

  24. Hi I’d like to make these for a 1st birthday, not sure about honey yet. Could I substitute maple syrup for honey? If so how much would you use?

    • dani stout Reply

      Hmm, you could try it. I’d think equal amounts? Not sure as I haven’t tried it.

  25. My frosting is lumpy and not smooth, I’m going to try adding more cream cheese because it’s a little runnyy as well but why would it be lumpy?

  26. Alyssa Mackelprang Reply

    In regards to the cream cheese frosting. Since everything needs to be cold to make it, does it loose it’s form and ooze if left out for very long? Could I get away with putting them out for a bridal shower and count on the frosting staying formed for a good 1.5-2 hours?

  27. The honey isn’t raw if you bake it. In fact, you destroy any healthful benefits. I never understood this with these healthy recipes. You heat the honey and you turn it into nothing better than regular sugar. Worse, even, because of the higher fructose content. You should use maple for the cupcakes and raw honey for icing (because it never gets heated and thus retains the healthful properties of raw honey – like the enzymes).

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