
Paleo Pumpkin Muffins or Cupcakes are the essence of fall. I don’t even really like most things pumpkin, but this recipe I am in love with. It’s easy, it’s seasonal, and always enjoyed! Even if pumpkin spice everything is not your thing, I dare you to try these and not admit they are delicious.
Why We Love These Paleo Pumpkin Muffins or Cupcakes
I mean, have you ever wondered what the difference was between muffins and cupcakes? Usually just additional sugar in the batter and frosting on top! So, I give you the option to take this delicious paleo batter in whatever direction you want it! Want a fun after-school snack with less sugar? Make the muffin version, tossing in mini chocolate chips if desired. Or, want a seasonal dessert everyone will love? Turn them into cupcakes with my delicious dairy-free cream cheese frosting!
Plus, the recipe is versatile in that it includes two sets of options for flour, depending on your budget and food sensitivities. And, I’m happy to say one of the flour options makes these nut-free. With this recipe being gluten-free, dairy-free, and grain-free + that nut-free option = a perfect treat for a variety of dietary needs.

Ingredients
- Pumpkin puree – I usually use canned pumpkin puree. I find that in the baking aisle at most grocery stores. Or, if you have pumpkins you need to use up, you can make your own pureed pumpkin with a recipe like this one.
- Eggs – Large eggs are my standard. I do not have an egg replacement worked out for this recipe. If you find one that worked well for you, please drop it into the comments section!
- Oil – I usually use extra light-tasting olive oil or melted (but not hot) coconut oil. You can also use avocado oil or melted ghee. Ghee is not my favorite, as I feel the flavor is too strong often in baked goods, but it’s an option if you need it!
- Coconut sugar – I get my coconut sugar most affordably from the bulk bins at Winco. When I buy it online, here (1.5 pounds) or here (5lbs, cheaper but in bulk) are the one I get from Amazon. Can swap an equal amount of granulated monk fruit sugar if you need more of a Keto variety.

- Flour – Use just cassava flour for a single-ingredient nut-free option. Or use the two-flour combination of almond flour + tapioca flour which I think gives the best flavor and texture results. With almond flour, I prefer “super-fine” almond flour to get the best texture. I like this one from Blue Diamond I can get at Sam’s Club or Amazon. For tapioca flour, I get mine from the bulk bins at Winco. You can also find it easily on Amazon here. (NOTE: You will not use the Almond flour + Tapioca flour at all if you are using the nut-free Cassava flour option!) If you want a nut-free flour option, I include a cassava flour variation. Cassava flour is pretty dense, so you will use less of it than the combined flours. I get my cassava flour most often from Amazon.
- Pumpkin Pie Spice – Found in the baking aisle for the perfect pumpkin pie flavor. Or, you can always make your own pumpkin pie spice blend with a recipe like this one.
- Baking powder
- Salt – Just regular table salt here.


Paleo Pumpkin Muffins or Cupcakes
Ingredients
Option 1 (nut-free + single flour)
- 1 cup pumpkin puree
- 2 large eggs
- 1/4 cup oil
- 1/2-1 cup coconut sugar see notes below
- 3/4 cup cassava flour see other option below
- 1 1/2 teaspoon pumpkin pie spice
- 1 teaspoon baking powder
- 1/2 teaspoon salt
Option 2 (my favorite, combination flour)
- 1 cup pumpkin puree
- 2 large eggs
- 1/4 cup light tasting olive oil
- 1/2-1 cup coconut sugar see notes below
- 1 1/2 cup almond flour
- 1/2 cup tapioca flour preferred, but can sub arrowroot or potato starch
- 1 1/2 teaspoon pumpkin pie spice
- 1 teaspoon baking powder
- 1/2 teaspoon salt
Optional add-ons
- 1/2 cup dairy-free chocolate chips optional
Instructions
- Preheat oven to 350 degrees. Prepare muffin tin by lining with muffin wrappers or spray with cooking spray.
- Combine all wet ingredients (puree, eggs, oil) and sugar in a medium mixing bowl.
- Add all dry ingredients to wet ingredients and stir till just combined.
- If using chocolate chips, gently stir those in.
- Divide evenly among 12 muffin cups. Bake at 350 for 20-23 minutes, until top of the muffin bounces back when touched.
- Cool and enjoy! Top with dairy-free cream cheese frosting (below) if desired.
- TO FREEZE: Freeze in a single layer (once cooled) and then store in a sealed ziplock or container for up to 3 months.
Notes
Nutrition

Dairy-free Cream Cheese Frosting
Ingredients
- 4 ounces dairy-free cream cheese Kite Hill and Violife (nut-free) are my favorites
- 1/2 cup vegan butter softened; recommended for best flavor, but can use ghee
- 2 teaspoons vanilla
- 4 /12 - 5 cups powdered sugar or powdered monk fruit sugar (for Paleo or Keto)
Instructions
- Make frosting by beating together cream cheese, ghee or vegan butter, and vanilla in a medium bowl until well combined. Gradually add in powdered sugar until it reaches spreading consistency.
- If frosting is too dry or thick, add 1-2 tablespoons dairy-free milk. If it's too thin, add another 1/4 cup powdered sugar.















This the BEST recipe(s) for Pumpkin Muffins/Cupcakes! I’ve used both versions – I use the almond flour one the most only because I have more almond flour than cassava in my pantry. Only thing I did different was to use regular sugar instead of coconut sugar because that’s what I buy – I buy all my baking ingredients in bulk from Azure so I use up what I have first. I did sprinkle some brown sugar on top just for color. I make these for my grandkids that can’t have gluten & dairy – they absolutely love them and so do those of us who can have gluten & dairy! PERFECT RECIPES!!!
This makes me so happy to hear! I love that you made these for your grandkids and made it work with what you had on hand. Thank you so much for the comment, those help me so much!
We LOVE your recipes and I can’t wait to try this one! 😊 Think I could use pure stevia extract powder vs coconut sugar?
So happy you are loving my recipes, thank you! Great question but I haven’t used stevia extract powder a lot, so I can’t weigh in on how that substitute would turn out. LMK if you try it!
I am hoping to travel with these cupcakes. Do you think they’d travel well with frosting on? Thanks!
Great question. Yes, I have traveled with these successfully with frosting on, in a cupcake carrier. You can also always freeze them first before travel to ensure they travel well. Enjoy!
Thanks for another great recipe Autumn! Can I use all-purpose flour in place of the Cassava flour?
Yay, thank you! So glad you enjoyed it!
Great question on the all-purpose flour, but they really don’t behave the same (unfortunately). I would have to do further testing to know the amount needed and how it would turn out. Let me know if you try it!
Thank you for this simple recipe. The simple step by step instructions and notes were so helpful. Thank you! My family LOVED it!!
WOOT WOOT that your family loved this easy recipe! I’m so happy to hear it. Thank you for the review!
So yummy!! Used the almond and tapioca flour combo, also subbed with 2 flax eggs and added 1/2 tsp baking soda and my kids and I LOVE them! Thank you so much!
Thrilled to hear you loved it and that it was a family favorite. And I love hearing what substitutions worked for you, I know many need those egg-free options – wonderful the flax eggs were a success. Thanks so much for your kind review!
Another hit! Easy and tasty recipe. My family eats them quicker than I can make them. I have made dozens of the muffins.
I love that you have made these often and they are so loved! YAY! Thank you so much for the review.
thanks for this recipe! trying tomorrow! just do you know cassava flour can be found VERY cheaply at Asian and African grocery stores. its a common ingredient in there cuisine so its not seen as a “special healthy ingredient”. I literally buy it for like $2 a pound or so.
Oh interesting! I don’t have any of those grocery stores in my area, but will definitely seek it out – that’s amazing it’s so cheap there! Thank you for sharing.