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Unbelievably moist, beautifully spiced, lightly sweetened, and topped with the most delightful crumb topping – these easy pumpkin muffins are truly autumn in a baked good. Not only are they mouthwateringly delicious, they’re also naturally paleo, gluten free, grain free, and dairy free. No one would ever guess it, though! Once you try our pumpkin muffin recipe, you’ll never need another store-bought muffin mix ever again.

Two pumpkin muffins with a spiced crumb topping stacked on top of each other, with other muffins out of focus in the background.

🍂 What Makes This Recipe So Good

  • Pumpkin muffins are maybe the most quintessentially autumn baked good you could possibly come up with. Soft and fluffy and moist, made with real pumpkin and perfectly spiced with cinnamon, nutmeg, ginger, and clove. And, since they’re muffins and not cupcakes, there’s just the right amount of subtle sweetness both in the muffin itself and in the spiced crumble topping.
  • Speaking of the spiced crumb topping, I can’t tell you just how next-level that simple little touch is. It’s an extra boost of sweetness and spice, with a tiny bit of salt to wake up your tastebuds and amplify all the other flavors. Plus, it crisps up so beautifully in the oven, giving the muffin tops the lightest little crunch. Pumpkin muffins without a crumb topping are super tasty, don’t get me wrong, but once you try them with it? You’ll never go back.
  • If you tasted these muffins without seeing the ingredients list, you would NEVER suspect that they’re completely paleo, completely gluten free, and completely dairy free. Dare I say these could be considered… healthy pumpkin muffins? The fine-tuned blend of almond flour, coconut flour, and tapioca starch gives them that perfect muffin texture. Coconut sugar, with its lower glycemic index, makes them sweet without causing a big blood sugar surge. Instead of butter, refined coconut oil makes the muffins super moist without adding dairy. (I know “coconut” was mentioned a lot, but don’t worry! I promise these muffins taste nothing like coconut, just warm pumpkin spice gourdness. Er… goodness.)

👩🏼‍🍳 Chef’s Tips

  • To keep the pumpkin muffins paleo, be sure you’re using pumpkin purée and NOT canned pumpkin pie filling! Canned pumpkin purée is literally just that – puréed pumpkin, in a can. On the other hand, pie filling (or you may see it as pumpkin pie mix) is pumpkin plus spices and sugar. Regular sugar isn’t compatible with a paleo eating style, obviously. Even if you’re not paleo, you still don’t want to use pumpkin pie mix. You won’t be able to really account for the amount of spices used in the filling (especially since it can differ from brand to brand!) so your pumpkin muffins could end up way over-spiced.
  • Typically, cupcakes use liners and muffins don’t. I like to use liners for muffins, though, because they just make everything that much easier. If you don’t have parchment paper liners on hand, you can totally DIY some out of parchment paper! Check out the easy how-to below.
  • For healthy pumpkin muffins that are over-the-top soft and moist, let the batter rest. Cover the bowl with a lid or plastic wrap and refrigerate it for at least 30 minutes. Letting the batter rest gives the flours more time to absorb the liquids, which will help you avoid a sandy or gritty texture. After resting, scoop the cold batter into the muffin tin and bake according to the original instructions below.
  • It is possible to over-mix the pumpkin muffin batter, so be really careful not to! Mixing the batter too much will make it dense and thick. If that happens, you won’t get as much rise on the muffins, and they might not have their dreamy texture.

📄 How to Make Your Own Parchment Paper Muffin Liners

  1. Cut parchment paper into one dozen 5-inch by 5-inch squares.
  2. Center a square over one of the muffin pan’s cavities, then press the square straight down into the bottom of the cavity. You can use your hand, or use a cup that fits in the bottom of the muffin cavity perfectly. Even a canned good would work if it’s the right size.
  3. Gently twist whatever you’re using to press the paper, then remove the object, leaving the paper in the muffin tin. The corners of the paper square will stick up and out of the muffin cavity, and the bottom and sides of the muffin cavity should be covered by the paper.
  4. Repeat with the remaining parchment squares!
A pumpkin muffin, with the paper lining peeled down and a large bite missing from the front side of the muffin. More whole muffins stand in the background.

🍎 Seasonal Recipes Fit for Fall

Recipe By: Cheryl Malik
5 from 29 votes

Pumpkin Muffins with a Spiced Crumb Topping

Prep 20 minutes
Cook 30 minutes
Total 50 minutes
Perfectly pumpkin muffins, lightly sweetened with coconut sugar and deliciously spiced with the season's finest flavors. Naturally paleo, gluten free, grain free, and dairy free!
12 pumpkin muffins


  • Oven
  • metal 12-cup muffin pan
  • 12 parchment paper muffin liners store-bought or make your own (see Notes)
  • small mixing bowl
  • Fork
  • refrigerator
  • medium mixing bowl
  • 2 whisks
  • Small microwave-safe bowl
  • Spoon or small silicone spatula
  • large mixing bowl
  • Cookie scoop with release handle or large spoon or measuring cup
  • toothpicks or butter knife
  • wire cooling rack


For the Spiced Crumb Topping

  • 2 tablespoons refined coconut oil at room temperature
  • 4 tablespoons fine almond flour blanched or unblanched
  • 4 tablespoons coconut sugar see Notes
  • ½ teaspoon ground cinnamon
  • ¼ teaspoon pumpkin pie spice store-bought or make your own
  • 1 pinch salt

For the Pumpkin Muffins (Dry Ingredients)

For the Pumpkin Muffins (Wet Ingredients)


  • Preheat oven to 325° Fahrenheit. Position oven racks so muffin tin will sit in center of oven. Line muffin tin with parchment paper liners and set aside.

For the Spiced Crumb Topping

  • Add 2 tablespoons refined coconut oil, 4 tablespoons fine almond flour, 4 tablespoons coconut sugar, ½ teaspoon ground cinnamon, ¼ teaspoon pumpkin pie spice, and 1 pinch salt to small mixing bowl.
    Ingredients for pumpkin muffin crumb topping in a white bowl with a fork.
  • Use fork to combine ingredients until fully incorporated and crumbly. Place bowl in refrigerator and chill until ready to use.
    Pumpkin muffin crumb topping mixture in a small bowl with a fork.

For the Pumpkin Muffin Batter

  • Add 2 cups fine blanched almond flour, ½ cup tapioca starch, ¼ cup coconut flour, ¼ teaspoon sea salt, ½ cup coconut sugar, 1 teaspoon ground cinnamon, 1 teaspoon pumpkin pie spice, and 1 ½ teaspoons fresh baking soda to medium mixing bowl.
    Dry ingredients for pumpkin muffins in a large glass mixing bowl with a silver whisk resting in the bowl.
  • Whisk ingredients together until well blended, with no lumps remaining. Set bowl aside.
    Dry ingredients for pumpkin muffins in a large glass mixing bowl with a silver whisk resting in the bowl.
  • Place ½ cup refined coconut oil in small microwave-safe bowl. Place bowl in microwave and heat oil in 15-second increments, stirring between each, until oil is melted. Carefully remove bowl from microwave and set aside. Let oil cool until no longer hot, but not cool enough to solidify again.
  • While oil cools, crack 3 large eggs into large mixing bowl. Lightly whisk eggs until well combined. Add cooled oil to large bowl with beaten eggs, followed by ¼ cup unsweetened almond milk, 2 teaspoons pure vanilla extract, and 1 cup canned pumpkin purée.
  • Slowly add dry ingredients to bowl of wet ingredients in small increments, gently whisking between each addition to just incorporate dry ingredients into wet. Continue until all wet and dry ingredients are fully combined into muffin batter. Be careful not overmix batter or muffins will be dense.
    Prepared batter for pumpkin muffins in a large glass mixing bowl with a silver whisk.

To Bake the Pumpkin Muffins

  • Use cookie scoop to portion muffin butter into prepared muffin tin, filling each muffin tin cavity equally. Batter should fill each cavity almost completely and be rounded on top.
  • Top each unbaked muffin with approximately 1 teaspoon of spiced crumb topping, sprinkling topping evenly over entire surface of muffin when possible. Add any remaining crumb topping as desired.
    Unbaked pumpkin muffin batter in a muffin tin cavity lined with parchment paper liner, topped with a spiced crumb topping.
  • Place muffin tin in preheated oven. Bake muffins 20 minutes, then begin checking doneness. Continue baking until toothpick inserted into center of muffin can be removed completely free of crumbs and when surface of muffin springs back when gently pressed. Exact bake times will vary.
  • When muffins are ready, carefully remove muffin tin from oven and set aside to cool 5 minutes.
  • After 5 minutes, remove muffins from tin and place on wire cooling rack. Let muffins cool to room temperature, then serve and enjoy.
  • Measuring Ingredients: Use the spoon-and-level method to measure out your larger-quantity dry ingredients. Instead of putting the measuring cup into the bag/container of flour or coconut sugar, use a spoon to transfer the flour or sugar out of the container and into the measuring cup. This method doesn’t pack the ingredient into the measuring cup, making your measurements more accurate.
  • Muffin Liners: To make your own muffin liners, cut 12 5×5 squares out of parchment paper and press the center of each square into a muffin pan cavity. The corners of the paper square will stick up and out of the pan cavity, but the bottom and sides of the cavity should be completely covered.
  • Baking Soda: The fresher the baking soda, the more effective it is. If your baking soda is older than 6 months, buy new baking soda for this recipe.
  • Pumpkin Purée: Be sure you’re using pumpkin purée and not pumpkin pie filling. Pumpkin pie filling usually has added sugars and spices which can throw off the flavors of the muffins (and may not be compatible with your specific diet).
  • Optional Step: After all ingredients are combined into the muffin batter, cover the bowl and refrigerate the batter at least 30 minutes, to give the starches in the dry ingredients more time to absorb the liquid ingredients.
  • Storage: Let muffins cool completely, then transfer leftover pumpkin muffins to airtight container. Store at room temperature up to 1 week.
  • Freezer Storage: Let muffins cool completely, then wrap each muffin in plastic wrap. Stand wrapped muffins on baking sheet or plate and place in freezer for 30 minutes. After 30 minutes, transfer wrapped muffins to airtight container or sealable freezer bag and place container or bag in freezer. Store frozen muffins up to 3 months. Defrost frozen muffins in fridge or at room temperature overnight before serving. Reheat in microwave to enjoy warm if desired.
  • Make it Lower Carb: Replace the coconut sugar with Brown Swerve.

Approximate Information for One Serving

Serving Size: 1 pumpkin muffinCalories: 306calProtein: 7gFat: 22gSaturated Fat: 10gTrans Fat: 0.01gCholesterol: 47mgSodium: 237mgPotassium: 273mgTotal Carbs: 22gFiber: 5gSugar: 10gNet Carbs: 17gVitamin A: 3246IUVitamin C: 1mgCalcium: 77mgIron: 2mg
Nutrition Disclaimers
Number of total servings shown is approximate. Actual number of servings will depend on your preferred portion sizes.
Nutritional values shown are general guidelines and reflect information for 1 serving using the ingredients listed, not including any optional ingredients. Actual macros may vary slightly depending on specific brands and types of ingredients used.
To determine the weight of one serving, prepare the recipe as instructed. Weigh the finished recipe, then divide the weight of the finished recipe (not including the weight of the container the food is in) by the desired number of servings. Result will be the weight of one serving.

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  1. Could you substitute regular milk for the almond milk?

    1. Megan | 40 Aprons Team Megan | 40 Aprons Team says:

      We didn’t test it with regular milk since it’s a dairy-free recipe, but that should work!

  2. These muffins were moist and full of flavor! Used a scooper to portion out into silicone mold muffin tray and they rose beautifully!5 stars

    1. Avatar Jessica | 40 Aprons Team says:

      So glad you loved the muffins, Hillary! 🙂

      1. SO excited to make these! Do you know if potato starch would work in place of the tapioca starch?

        1. Megan | 40 Aprons Team Megan | 40 Aprons Team says:

          We didn’t test that so we can’t say how it might turn out. If you try it, though, please report back and let us know how it goes!

  3. Half cup of coconut sugar??
    So sorry but I really wanted to like these but half cup sugar just didn’t make them sweet enough 🙁

    1. Megan | 40 Aprons Team Megan | 40 Aprons Team says:

      So sorry this didn’t do the trick for you, Lulu! Muffins typically aren’t very sweet, at least not as sweet as cupcakes, and since these muffins are designed to be paleo, they’re much less sweet than traditional baked goods might be. We do also try to avoid making our recipes overly-sweet whenever possible, so these were the right amount of sweet for us, but everyone’s tastes are different. You can always add more coconut sugar to your liking! I hope you’ll give this one another try.

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